diff --git a/.github/workflows/run_cell-type-nonETP-ALL-03.yml b/.github/workflows/run_cell-type-nonETP-ALL-03.yml
index 7880d3596..6315533c5 100644
--- a/.github/workflows/run_cell-type-nonETP-ALL-03.yml
+++ b/.github/workflows/run_cell-type-nonETP-ALL-03.yml
@@ -59,7 +59,8 @@ jobs:
             libfontconfig1-dev \
             libharfbuzz-dev \
             libfribidi-dev \
-            libtiff5-dev
+            libtiff5-dev \
+            jags
 
       - name: Set up renv
         uses: r-lib/actions/setup-renv@v2
@@ -87,7 +88,19 @@ jobs:
         run: |
           cd ${MODULE_PATH}
           # run module script(s) here
+          printf "\n\nRunning 00-01_processing_rds.R\n"
           Rscript scripts/00-01_processing_rds.R
+          printf "\n\nRunning 02-03_annotation.R\n"
           Rscript scripts/02-03_annotation.R
+          printf "\n\nRunning 04_multipanel_plot.R\n"
           Rscript scripts/04_multipanel_plot.R
+          printf "\n\nRunning 05_cluster_evaluation.R\n"
           Rscript scripts/05_cluster_evaluation.R
+          printf "\n\nRunning 06_sctype_exploration.R\n"
+          Rscript scripts/06_sctype_exploration.R
+          printf "\n\nRunning 07_run_copykat.R\n"
+          Rscript scripts/07_run_copykat.R
+          printf "\n\nRunning markerGenes_submission.R\n"
+          Rscript scripts/markerGenes_submission.R
+          printf "\n\nRunning writeout_submission.R\n"
+          Rscript scripts/writeout_submission.R
diff --git a/analyses/cell-type-nonETP-ALL-03/Dockerfile b/analyses/cell-type-nonETP-ALL-03/Dockerfile
index dffa86a9b..ce6ff54bb 100644
--- a/analyses/cell-type-nonETP-ALL-03/Dockerfile
+++ b/analyses/cell-type-nonETP-ALL-03/Dockerfile
@@ -52,6 +52,9 @@ RUN conda-lock install -n ${ENV_NAME} conda-lock.yml \
 # Copy the renv.lock file from the host environment to the image
 COPY renv.lock renv.lock
 
+# Temporarily install Rhtslib separately
+RUN Rscript -e 'BiocManager::install("Rhtslib")'
+
 # restore from renv.lock file and clean up to reduce image size
 RUN Rscript -e 'renv::restore()' \
   && rm -rf ~/.cache/R/renv \
diff --git a/analyses/cell-type-nonETP-ALL-03/README.md b/analyses/cell-type-nonETP-ALL-03/README.md
index cc6045588..e3502fec3 100644
--- a/analyses/cell-type-nonETP-ALL-03/README.md
+++ b/analyses/cell-type-nonETP-ALL-03/README.md
@@ -8,9 +8,11 @@ We first aim to annotate the cell types in non-ETP T-ALL, and use the annotated
 
 -   We use the cell type marker (`Azimuth_BM_level1.csv`) from [Azimuth Human Bone Marrow reference](https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow). In total, there are 14 cell types: B, CD4T, CD8T, Other T, DC, Monocytes, Macrophages, NK, Early Erythrocytes, Late Erythrocytes, Plasma, Platelet, Stromal, and Hematopoietic Stem and Progenitor Cells (HSPC). Based on the exploratory analysis, we believe that most of the cells in these samples do not express adequate markers to be distinguished at finer cell type level (eg. naive vs memory, CD14 vs CD16 etc.), and majority of the cells should belong to T-cells. In addition, we include the marker genes for blast cell [[Bhasin et al. (2023)](https://www.nature.com/articles/s41598-023-39152-z)] as well as erythroid precursor and cancer cell in immune system [[ScType](https://sctype.app/database.php) database].
 
+    \*\*`Azimuth_BM_level1.csv` is converted to `submission_markerGenes.tsv`, in the final submission format.
+
 -   Since ScType annotates cell types at cluster level using marker genes provided by user or from the built-in database, we employ [self-assembling manifold](https://github.com/atarashansky/self-assembling-manifold/tree/master) (SAM) algorithm, a soft feature selection strategy for better separation of homogeneous cell types.
 
--   After cell type annotation, we provide B cells as the normal cells in the sample, if there is any, to [CopyKat](https://github.com/navinlabcode/copykat), for identification of tumor cells.
+-   After cell type annotation, we fine-tune the annotated B cells by applying 99 percentile cutoff of non-B ScType score on the "B cell clusters". We then use the new B cells (i.e those cells which passed the cutoff) as the normal cells in running [CopyKat](https://github.com/navinlabcode/copykat), for the identification of tumor cells. We could not detect strong B cell signal in `SCPCL000082`.
 
 Here are the steps in the module:
 
@@ -18,6 +20,10 @@ Here are the steps in the module:
 
 2.  Annotating cell type using ScType and identifying tumor cells using CopyKat (`scripts/02-03_annotation.R`)
 
+3.  Fine-tuning the B cells (`scripts/06_sctype_exploration.R`)
+
+4.  Re-running CopyKat (`scripts/07_run_copykat.R`)
+
 ## Usage
 
 Before running Rscripts in R or Rstudio, we first need to prepare the input files as shown in the next section, and run the following codes in the terminal for installing required libraries:
@@ -44,21 +50,15 @@ The `scripts/00-01_processing_rds.R` requires the processed SingleCellExperiment
 
 As for the annotation, `scripts/02-03_annotation.R` requires cell type marker gene file, `Azimuth_BM_level1.csv`, as an input for ScType. This excel file contains a list of positive marker genes in Ensembl ID under `ensembl_id_positive_marker` for each cell type; *TMEM56* and *CD235a* are not detected in our dataset, thus they are being removed as part of the markers for Late Eryth and Pre Eryth respectively. As of now, there is no negative marker genes provided under `ensembl_id_negative_marker`.
 
-## Output files
-
-Running `scripts/00-01_processing_rds.R` will generate two types of output:
-
--   `rds` objects in `scratch/`
-
--   umap plots showing leiden clustering in `plots/`
+## Important output files
 
-Running `scripts/02-03_annotation.R` will generate several outputs:
+-   `rds` objects in `results/rds`
 
--   updated `rds` objects in `scratch/`
+-   ScType results of top 10 possible cell types in a cluster (`results/_sctype_top10_celltypes_perCluster.txt`) and ScType score (`results/_sctype_scores.txt`)
 
--   umap plots showing cell type and CopyKat prediction (if there is any) and dotplots showing the features added with `AddModuleScore()` in `plots/`
+-   location of fine-tuned B cells in umap (`plots/sctype_exploration/_newBcells.png`) and the cell type assignment with added fine-tuned B cells (`results/_newB-normal-annotation.txt`)
 
--   ScType results of top 10 possible cell types in a cluster (`_sctype_top10_celltypes_perCluster.txt`) and metadata file tabulating leiden cluster, cell type, low confidence cell type, and CopyKat prediction for each cell (`_metadata.txt`) in `results/`
+-   final submission table (`results/submission_table/_metadata.tsv`) and the umap plots showing cell_type_assignment from ScType and tumor_cell_classification from CopyKat using fine-tuned B cells (`results/submission_table/multipanels_.png`)
 
 ## Software requirements
 
diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000076_blastModuleScore.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000076_blastModuleScore.png
index c17dd4f95..16ef89395 100644
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000076_celltypeVScopykat.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000076_celltypeVScopykat.png
index c6a20075a..41ead1823 100644
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000077_blastModuleScore.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000077_blastModuleScore.png
new file mode 100644
index 000000000..07fc4f059
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000077_celltypeVScopykat.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000077_celltypeVScopykat.png
new file mode 100644
index 000000000..71ae1572c
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000078_blastModuleScore.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000078_blastModuleScore.png
index 4f7e0581c..110407d11 100644
Binary files a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000078_blastModuleScore.png and b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000078_blastModuleScore.png differ
diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000078_celltypeVScopykat.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000078_celltypeVScopykat.png
index 2a4ace4e0..51383301c 100644
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000079_blastModuleScore.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000079_blastModuleScore.png
index c3c82e1bb..8a82ce323 100644
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000079_celltypeVScopykat.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000079_celltypeVScopykat.png
index c4e8beb0d..bd3cbf8e9 100644
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000080_blastModuleScore.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000080_blastModuleScore.png
index f68b799eb..475425f9f 100644
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000080_celltypeVScopykat.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000080_celltypeVScopykat.png
index bc87e54db..95ef7fc15 100644
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000081_blastModuleScore.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000081_blastModuleScore.png
index eae6b7b59..fb3fe71d2 100644
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000081_celltypeVScopykat.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000081_celltypeVScopykat.png
index 3b6385348..36fd636cc 100644
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000703_blastModuleScore.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000703_blastModuleScore.png
index 8312e8808..520187dd8 100644
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000703_celltypeVScopykat.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000703_celltypeVScopykat.png
index d49cf1548..10f793e62 100644
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000704_blastModuleScore.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000704_blastModuleScore.png
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new file mode 100644
index 000000000..a241fbb38
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index a52926f25..35abc03b0 100644
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000706_celltypeVScopykat.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000706_celltypeVScopykat.png
index c154287ad..b8a68af2d 100644
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000710_blastModuleScore.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000710_blastModuleScore.png
new file mode 100644
index 000000000..f53c7f504
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000710_celltypeVScopykat.png b/analyses/cell-type-nonETP-ALL-03/plots/copykat_exploration/SCPCL000710_celltypeVScopykat.png
new file mode 100644
index 000000000..255b2536e
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diff --git a/analyses/cell-type-nonETP-ALL-03/plots/SCPCL000077-SCPCL000703_splitPlot.png b/analyses/cell-type-nonETP-ALL-03/plots/merging/SCPCL000077-SCPCL000703_splitPlot.png
similarity index 100%
rename from analyses/cell-type-nonETP-ALL-03/plots/SCPCL000077-SCPCL000703_splitPlot.png
rename to analyses/cell-type-nonETP-ALL-03/plots/merging/SCPCL000077-SCPCL000703_splitPlot.png
diff --git a/analyses/cell-type-nonETP-ALL-03/plots/SCPCL000082-SCPCL000703_splitPlot.png b/analyses/cell-type-nonETP-ALL-03/plots/merging/SCPCL000082-SCPCL000703_splitPlot.png
similarity index 100%
rename from analyses/cell-type-nonETP-ALL-03/plots/SCPCL000082-SCPCL000703_splitPlot.png
rename to analyses/cell-type-nonETP-ALL-03/plots/merging/SCPCL000082-SCPCL000703_splitPlot.png
diff --git a/analyses/cell-type-nonETP-ALL-03/plots/SCPCL000704-SCPCL000703_splitPlot.png b/analyses/cell-type-nonETP-ALL-03/plots/merging/SCPCL000704-SCPCL000703_splitPlot.png
similarity index 100%
rename from analyses/cell-type-nonETP-ALL-03/plots/SCPCL000704-SCPCL000703_splitPlot.png
rename to analyses/cell-type-nonETP-ALL-03/plots/merging/SCPCL000704-SCPCL000703_splitPlot.png
diff --git a/analyses/cell-type-nonETP-ALL-03/plots/SCPCL000706-SCPCL000703_splitPlot.png b/analyses/cell-type-nonETP-ALL-03/plots/merging/SCPCL000706-SCPCL000703_splitPlot.png
similarity index 100%
rename from analyses/cell-type-nonETP-ALL-03/plots/SCPCL000706-SCPCL000703_splitPlot.png
rename to analyses/cell-type-nonETP-ALL-03/plots/merging/SCPCL000706-SCPCL000703_splitPlot.png
diff --git a/analyses/cell-type-nonETP-ALL-03/plots/SCPCL000710-SCPCL000703_splitPlot.png b/analyses/cell-type-nonETP-ALL-03/plots/merging/SCPCL000710-SCPCL000703_splitPlot.png
similarity index 100%
rename from analyses/cell-type-nonETP-ALL-03/plots/SCPCL000710-SCPCL000703_splitPlot.png
rename to analyses/cell-type-nonETP-ALL-03/plots/merging/SCPCL000710-SCPCL000703_splitPlot.png
diff --git a/analyses/cell-type-nonETP-ALL-03/plots/multipanels_SCPCL000077-SCPCL000703.png b/analyses/cell-type-nonETP-ALL-03/plots/merging/multipanels_SCPCL000077-SCPCL000703.png
similarity index 100%
rename from analyses/cell-type-nonETP-ALL-03/plots/multipanels_SCPCL000077-SCPCL000703.png
rename to analyses/cell-type-nonETP-ALL-03/plots/merging/multipanels_SCPCL000077-SCPCL000703.png
diff --git a/analyses/cell-type-nonETP-ALL-03/plots/multipanels_SCPCL000082-SCPCL000703.png b/analyses/cell-type-nonETP-ALL-03/plots/merging/multipanels_SCPCL000082-SCPCL000703.png
similarity index 100%
rename from analyses/cell-type-nonETP-ALL-03/plots/multipanels_SCPCL000082-SCPCL000703.png
rename to analyses/cell-type-nonETP-ALL-03/plots/merging/multipanels_SCPCL000082-SCPCL000703.png
diff --git a/analyses/cell-type-nonETP-ALL-03/plots/multipanels_SCPCL000704-SCPCL000703.png b/analyses/cell-type-nonETP-ALL-03/plots/merging/multipanels_SCPCL000704-SCPCL000703.png
similarity index 100%
rename from analyses/cell-type-nonETP-ALL-03/plots/multipanels_SCPCL000704-SCPCL000703.png
rename to analyses/cell-type-nonETP-ALL-03/plots/merging/multipanels_SCPCL000704-SCPCL000703.png
diff --git a/analyses/cell-type-nonETP-ALL-03/plots/multipanels_SCPCL000706-SCPCL000703.png b/analyses/cell-type-nonETP-ALL-03/plots/merging/multipanels_SCPCL000706-SCPCL000703.png
similarity index 100%
rename from analyses/cell-type-nonETP-ALL-03/plots/multipanels_SCPCL000706-SCPCL000703.png
rename to analyses/cell-type-nonETP-ALL-03/plots/merging/multipanels_SCPCL000706-SCPCL000703.png
diff --git a/analyses/cell-type-nonETP-ALL-03/plots/multipanels_SCPCL000710-SCPCL000703.png b/analyses/cell-type-nonETP-ALL-03/plots/merging/multipanels_SCPCL000710-SCPCL000703.png
similarity index 100%
rename from analyses/cell-type-nonETP-ALL-03/plots/multipanels_SCPCL000710-SCPCL000703.png
rename to analyses/cell-type-nonETP-ALL-03/plots/merging/multipanels_SCPCL000710-SCPCL000703.png
diff --git a/analyses/cell-type-nonETP-ALL-03/renv.lock b/analyses/cell-type-nonETP-ALL-03/renv.lock
index 708c6c33b..84ed5a126 100644
--- a/analyses/cell-type-nonETP-ALL-03/renv.lock
+++ b/analyses/cell-type-nonETP-ALL-03/renv.lock
@@ -66,6 +66,20 @@
       ],
       "Hash": "ef32d07aafdd12f24c5827374ae3590d"
     },
+    "BiocIO": {
+      "Package": "BiocIO",
+      "Version": "1.14.0",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "BiocGenerics",
+        "R",
+        "S4Vectors",
+        "methods",
+        "tools"
+      ],
+      "Hash": "f97a7ef01d364cf20d1946d43a3d526f"
+    },
     "BiocManager": {
       "Package": "BiocManager",
       "Version": "1.30.25",
@@ -121,6 +135,26 @@
       ],
       "Hash": "b892e27fc9659a4c8f8787d34c37b8b2"
     },
+    "Biostrings": {
+      "Package": "Biostrings",
+      "Version": "2.72.1",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "BiocGenerics",
+        "GenomeInfoDb",
+        "IRanges",
+        "R",
+        "S4Vectors",
+        "XVector",
+        "crayon",
+        "grDevices",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "886ff0ed958d6f839ed2e0d01f6853b3"
+    },
     "DelayedArray": {
       "Package": "DelayedArray",
       "Version": "0.30.1",
@@ -143,13 +177,13 @@
     },
     "FNN": {
       "Package": "FNN",
-      "Version": "1.1.4",
+      "Version": "1.1.4.1",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R"
       ],
-      "Hash": "eaabdc7938aa3632a28273f53a0d226d"
+      "Hash": "c7b4a49c7f435d0a67bb1e127e953d75"
     },
     "GenomeInfoDb": {
       "Package": "GenomeInfoDb",
@@ -179,9 +213,31 @@
       ],
       "Hash": "c3c792a7b7f2677be56e8632c5b7543d"
     },
+    "GenomicAlignments": {
+      "Package": "GenomicAlignments",
+      "Version": "1.40.0",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "BiocGenerics",
+        "BiocParallel",
+        "Biostrings",
+        "GenomeInfoDb",
+        "GenomicRanges",
+        "IRanges",
+        "R",
+        "Rsamtools",
+        "S4Vectors",
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     "munsell": {
       "Package": "munsell",
       "Version": "0.5.1",
@@ -1869,6 +2315,17 @@
       ],
       "Hash": "4fd8900853b746af55b81fda99da7695"
     },
+    "mvtnorm": {
+      "Package": "mvtnorm",
+      "Version": "1.3-1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "stats"
+      ],
+      "Hash": "77c61d51ce0f36e3c1a76e6b295aab31"
+    },
     "nlme": {
       "Package": "nlme",
       "Version": "3.1-164",
@@ -1885,13 +2342,25 @@
     },
     "openssl": {
       "Package": "openssl",
-      "Version": "2.2.1",
+      "Version": "2.2.2",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "askpass"
       ],
-      "Hash": "c62edf62de70cadf40553e10c739049d"
+      "Hash": "d413e0fef796c9401a4419485f709ca1"
+    },
+    "optparse": {
+      "Package": "optparse",
+      "Version": "1.7.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "getopt",
+        "methods"
+      ],
+      "Hash": "ce5f8381cd2c38d1fc14c83d8b21efd0"
     },
     "parallelDist": {
       "Package": "parallelDist",
@@ -1959,6 +2428,17 @@
       ],
       "Hash": "51e3a7a4af0b863e5d380575cbd33cda"
     },
+    "phyclust": {
+      "Package": "phyclust",
+      "Version": "0.1-34",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "ape"
+      ],
+      "Hash": "18a29354ea762dd01042d8697b7089d4"
+    },
     "pillar": {
       "Package": "pillar",
       "Version": "1.9.0",
@@ -2049,6 +2529,30 @@
       ],
       "Hash": "5879bf5aae702ffef0a315c44328f984"
     },
+    "prettyunits": {
+      "Package": "prettyunits",
+      "Version": "1.2.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7"
+    },
+    "progress": {
+      "Package": "progress",
+      "Version": "1.2.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "crayon",
+        "hms",
+        "prettyunits"
+      ],
+      "Hash": "f4625e061cb2865f111b47ff163a5ca6"
+    },
     "progressr": {
       "Package": "progressr",
       "Version": "0.14.0",
@@ -2144,15 +2648,38 @@
       ],
       "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
     },
+    "readr": {
+      "Package": "readr",
+      "Version": "2.1.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "cli",
+        "clipr",
+        "cpp11",
+        "crayon",
+        "hms",
+        "lifecycle",
+        "methods",
+        "rlang",
+        "tibble",
+        "tzdb",
+        "utils",
+        "vroom"
+      ],
+      "Hash": "9de96463d2117f6ac49980577939dfb3"
+    },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.7",
+      "Version": "1.0.11",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "utils"
       ],
-      "Hash": "397b7b2a265bc5a7a06852524dabae20"
+      "Hash": "47623f66b4e80b3b0587bc5d7b309888"
     },
     "reshape2": {
       "Package": "reshape2",
@@ -2167,6 +2694,22 @@
       ],
       "Hash": "bb5996d0bd962d214a11140d77589917"
     },
+    "restfulr": {
+      "Package": "restfulr",
+      "Version": "0.0.15",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "RCurl",
+        "S4Vectors",
+        "XML",
+        "methods",
+        "rjson",
+        "yaml"
+      ],
+      "Hash": "44651c1e68eda9d462610aca9f15a815"
+    },
     "reticulate": {
       "Package": "reticulate",
       "Version": "1.39.0",
@@ -2212,6 +2755,27 @@
       ],
       "Hash": "99e15369f8fb17dc188377234de13fc6"
     },
+    "rjags": {
+      "Package": "rjags",
+      "Version": "4-16",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "coda"
+      ],
+      "Hash": "a36ff5b8df160527e29037be8e1cdf7d"
+    },
+    "rjson": {
+      "Package": "rjson",
+      "Version": "0.2.23",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "7a04e9eff95857dbf557b4e5f0b3d1a8"
+    },
     "rlang": {
       "Package": "rlang",
       "Version": "1.1.4",
@@ -2256,6 +2820,46 @@
       ],
       "Hash": "4c8415e0ec1e29f3f4f6fc108bef0144"
     },
+    "rtracklayer": {
+      "Package": "rtracklayer",
+      "Version": "1.64.0",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "BiocGenerics",
+        "BiocIO",
+        "Biostrings",
+        "GenomeInfoDb",
+        "GenomicAlignments",
+        "GenomicRanges",
+        "IRanges",
+        "R",
+        "Rsamtools",
+        "S4Vectors",
+        "XML",
+        "XVector",
+        "curl",
+        "httr",
+        "methods",
+        "restfulr",
+        "tools",
+        "zlibbioc"
+      ],
+      "Hash": "3d6f004fce582bd7d68e2e18d44abbc1"
+    },
+    "sandwich": {
+      "Package": "sandwich",
+      "Version": "3.1-1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "stats",
+        "utils",
+        "zoo"
+      ],
+      "Hash": "072bb2d27425f2a58fe71fe1080676ce"
+    },
     "sass": {
       "Package": "sass",
       "Version": "0.4.9",
@@ -2312,7 +2916,6 @@
       "RemoteHost": "api.github.com",
       "RemoteRepo": "schard",
       "RemoteUsername": "cellgeni",
-      "RemoteRef": "HEAD",
       "RemoteSha": "ac382a6bdfc0fff164064f8dd0f0c3e29d0a15fc",
       "Requirements": [
         "Matrix",
@@ -2440,9 +3043,9 @@
     },
     "spam": {
       "Package": "spam",
-      "Version": "2.10-0",
+      "Version": "2.11-0",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "Rcpp",
@@ -2450,7 +3053,7 @@
         "grid",
         "methods"
       ],
-      "Hash": "ffe1f9e95a4375530747b268f82b5086"
+      "Hash": "6581c0a0bb8594b85c8de869644174ac"
     },
     "spatstat.data": {
       "Package": "spatstat.data",
@@ -2582,6 +3185,18 @@
       ],
       "Hash": "69b26ceb9f7976f347049b4d470c2d65"
     },
+    "statmod": {
+      "Package": "statmod",
+      "Version": "1.5.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "graphics",
+        "stats"
+      ],
+      "Hash": "26e158d12052c279bdd4ba858b80fb1f"
+    },
     "stringi": {
       "Package": "stringi",
       "Version": "1.8.4",
@@ -2630,10 +3245,10 @@
     },
     "sys": {
       "Package": "sys",
-      "Version": "3.4.2",
+      "Version": "3.4.3",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "3a1be13d68d47a8cd0bfd74739ca1555"
+      "Repository": "RSPM",
+      "Hash": "de342ebfebdbf40477d0758d05426646"
     },
     "tensor": {
       "Package": "tensor",
@@ -2710,6 +3325,17 @@
       ],
       "Hash": "9db859e8aabbb474293dde3097839420"
     },
+    "tzdb": {
+      "Package": "tzdb",
+      "Version": "0.4.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cpp11"
+      ],
+      "Hash": "f561504ec2897f4d46f0c7657e488ae1"
+    },
     "utf8": {
       "Package": "utf8",
       "Version": "1.2.4",
@@ -2752,6 +3378,19 @@
       ],
       "Hash": "c03fa420630029418f7e6da3667aac4a"
     },
+    "viridis": {
+      "Package": "viridis",
+      "Version": "0.6.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "ggplot2",
+        "gridExtra",
+        "viridisLite"
+      ],
+      "Hash": "acd96d9fa70adeea4a5a1150609b9745"
+    },
     "viridisLite": {
       "Package": "viridisLite",
       "Version": "0.4.2",
@@ -2762,6 +3401,32 @@
       ],
       "Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
     },
+    "vroom": {
+      "Package": "vroom",
+      "Version": "1.6.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "bit64",
+        "cli",
+        "cpp11",
+        "crayon",
+        "glue",
+        "hms",
+        "lifecycle",
+        "methods",
+        "progress",
+        "rlang",
+        "stats",
+        "tibble",
+        "tidyselect",
+        "tzdb",
+        "vctrs",
+        "withr"
+      ],
+      "Hash": "390f9315bc0025be03012054103d227c"
+    },
     "withr": {
       "Package": "withr",
       "Version": "3.0.1",
@@ -2776,16 +3441,16 @@
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.47",
+      "Version": "0.48",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "grDevices",
         "stats",
         "tools"
       ],
-      "Hash": "36ab21660e2d095fef0d83f689e0477c"
+      "Hash": "89e455b87c84e227eb7f60a1b4e5fe1f"
     },
     "xtable": {
       "Package": "xtable",
diff --git a/analyses/cell-type-nonETP-ALL-03/renv/activate.R b/analyses/cell-type-nonETP-ALL-03/renv/activate.R
index d13f9932a..0eb51088a 100644
--- a/analyses/cell-type-nonETP-ALL-03/renv/activate.R
+++ b/analyses/cell-type-nonETP-ALL-03/renv/activate.R
@@ -2,7 +2,7 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.7"
+  version <- "1.0.11"
   attr(version, "sha") <- NULL
 
   # the project directory
@@ -98,6 +98,66 @@ local({
     unloadNamespace("renv")
 
   # load bootstrap tools   
+  ansify <- function(text) {
+    if (renv_ansify_enabled())
+      renv_ansify_enhanced(text)
+    else
+      renv_ansify_default(text)
+  }
+  
+  renv_ansify_enabled <- function() {
+  
+    override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA)
+    if (!is.na(override))
+      return(as.logical(override))
+  
+    pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA)
+    if (identical(pane, "build"))
+      return(FALSE)
+  
+    testthat <- Sys.getenv("TESTTHAT", unset = "false")
+    if (tolower(testthat) %in% "true")
+      return(FALSE)
+  
+    iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false")
+    if (tolower(iderun) %in% "false")
+      return(FALSE)
+  
+    TRUE
+  
+  }
+  
+  renv_ansify_default <- function(text) {
+    text
+  }
+  
+  renv_ansify_enhanced <- function(text) {
+  
+    # R help links
+    pattern <- "`\\?(renv::(?:[^`])+)`"
+    replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`"
+    text <- gsub(pattern, replacement, text, perl = TRUE)
+  
+    # runnable code
+    pattern <- "`(renv::(?:[^`])+)`"
+    replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`"
+    text <- gsub(pattern, replacement, text, perl = TRUE)
+  
+    # return ansified text
+    text
+  
+  }
+  
+  renv_ansify_init <- function() {
+  
+    envir <- renv_envir_self()
+    if (renv_ansify_enabled())
+      assign("ansify", renv_ansify_enhanced, envir = envir)
+    else
+      assign("ansify", renv_ansify_default, envir = envir)
+  
+  }
+  
   `%||%` <- function(x, y) {
     if (is.null(x)) y else x
   }
@@ -142,7 +202,10 @@ local({
     # compute common indent
     indent <- regexpr("[^[:space:]]", lines)
     common <- min(setdiff(indent, -1L)) - leave
-    paste(substring(lines, common), collapse = "\n")
+    text <- paste(substring(lines, common), collapse = "\n")
+  
+    # substitute in ANSI links for executable renv code
+    ansify(text)
   
   }
   
@@ -305,8 +368,11 @@ local({
       quiet    = TRUE
     )
   
-    if ("headers" %in% names(formals(utils::download.file)))
-      args$headers <- renv_bootstrap_download_custom_headers(url)
+    if ("headers" %in% names(formals(utils::download.file))) {
+      headers <- renv_bootstrap_download_custom_headers(url)
+      if (length(headers) && is.character(headers))
+        args$headers <- headers
+    }
   
     do.call(utils::download.file, args)
   
@@ -385,10 +451,21 @@ local({
     for (type in types) {
       for (repos in renv_bootstrap_repos()) {
   
+        # build arguments for utils::available.packages() call
+        args <- list(type = type, repos = repos)
+  
+        # add custom headers if available -- note that
+        # utils::available.packages() will pass this to download.file()
+        if ("headers" %in% names(formals(utils::download.file))) {
+          headers <- renv_bootstrap_download_custom_headers(repos)
+          if (length(headers) && is.character(headers))
+            args$headers <- headers
+        }
+  
         # retrieve package database
         db <- tryCatch(
           as.data.frame(
-            utils::available.packages(type = type, repos = repos),
+            do.call(utils::available.packages, args),
             stringsAsFactors = FALSE
           ),
           error = identity
@@ -470,6 +547,14 @@ local({
   
   }
   
+  renv_bootstrap_github_token <- function() {
+    for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) {
+      envval <- Sys.getenv(envvar, unset = NA)
+      if (!is.na(envval))
+        return(envval)
+    }
+  }
+  
   renv_bootstrap_download_github <- function(version) {
   
     enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
@@ -477,16 +562,16 @@ local({
       return(FALSE)
   
     # prepare download options
-    pat <- Sys.getenv("GITHUB_PAT")
-    if (nzchar(Sys.which("curl")) && nzchar(pat)) {
+    token <- renv_bootstrap_github_token()
+    if (nzchar(Sys.which("curl")) && nzchar(token)) {
       fmt <- "--location --fail --header \"Authorization: token %s\""
-      extra <- sprintf(fmt, pat)
+      extra <- sprintf(fmt, token)
       saved <- options("download.file.method", "download.file.extra")
       options(download.file.method = "curl", download.file.extra = extra)
       on.exit(do.call(base::options, saved), add = TRUE)
-    } else if (nzchar(Sys.which("wget")) && nzchar(pat)) {
+    } else if (nzchar(Sys.which("wget")) && nzchar(token)) {
       fmt <- "--header=\"Authorization: token %s\""
-      extra <- sprintf(fmt, pat)
+      extra <- sprintf(fmt, token)
       saved <- options("download.file.method", "download.file.extra")
       options(download.file.method = "wget", download.file.extra = extra)
       on.exit(do.call(base::options, saved), add = TRUE)
diff --git a/analyses/cell-type-nonETP-ALL-03/results/README.md b/analyses/cell-type-nonETP-ALL-03/results/README.md
index 11080bc8d..0c0fc2baa 100644
--- a/analyses/cell-type-nonETP-ALL-03/results/README.md
+++ b/analyses/cell-type-nonETP-ALL-03/results/README.md
@@ -12,8 +12,12 @@ These are the generated outputs for each sample in the S3 bucket:
 -   `rds` objects: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/rds`
 -   metadata and ScType results: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/`
 -   CopyKat results: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/copykat_output`
+-   InferCNV results: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/infercnv_output`
 -   evaluating cluster separation, stability, and purity: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/evalClus`
 -   umap and dot plots: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/plots`
 -   violin and stacked bar plots for exploring the results of CopyKat prediction: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/plots/copykat_exploration`
+-   ridge plots showing the ScType score for each cell type in annotated B cells from ScType, SingleR, and CellAssign, as well as the scatter plots showing the relationship between B cell ScType score and cluster purity of these cells: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/plots/sctype_exploration`
+-   ridge plots showing the ScType score for each cell type in fine-tuned B cells and feature plots showing the distribution of B cell ScType score: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/plots/sctype_exploration`
+-   final submission `tsv` files and `png` for cell type and/or tumor cell classification: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/submission_table`
 
 \*\*All the plots are also found in the repository plots/.
diff --git a/analyses/cell-type-nonETP-ALL-03/scripts/exploratory-analyses/sctype_exploration.R b/analyses/cell-type-nonETP-ALL-03/scripts/06_sctype_exploration.R
similarity index 100%
rename from analyses/cell-type-nonETP-ALL-03/scripts/exploratory-analyses/sctype_exploration.R
rename to analyses/cell-type-nonETP-ALL-03/scripts/06_sctype_exploration.R
diff --git a/analyses/cell-type-nonETP-ALL-03/scripts/07_run_copykat.R b/analyses/cell-type-nonETP-ALL-03/scripts/07_run_copykat.R
new file mode 100644
index 000000000..8a691df9b
--- /dev/null
+++ b/analyses/cell-type-nonETP-ALL-03/scripts/07_run_copykat.R
@@ -0,0 +1,35 @@
+#!/usr/bin/env Rscript
+
+library(Seurat)
+library(copykat)
+
+run_copykat <- function(ind.lib){
+  seu <- readRDS(file.path(out_loc,"results/rds",paste0(ind.lib,".rds")))
+  annot.file <- file.path(out_loc,"results",paste0(ind.lib,"_newB-normal-annotation.txt"))
+  if (file.exists(annot.file)){  #the sample has new B cells annotated
+    annot.df <- read.table(annot.file, header=F, row.names=1, sep="\t", stringsAsFactors=FALSE, 
+                           colClasses = c('character', 'character'))
+    norm.cells <- rownames(annot.df)[which(annot.df$V2=="new B")]
+    n_cores <- parallel::detectCores() - 1
+    copykat.test <- copykat(rawmat=seu@assays[["RNA"]]@counts, id.type="Ensemble",
+                            ngene.chr=5, win.size=25, KS.cut=0.1, sam.name=ind.lib,
+                            distance="euclidean", norm.cell.names=norm.cells,
+                            output.seg="FALSE", plot.genes="TRUE", genome="hg20",n.cores=n_cores)
+    idx <- match(colnames(seu), copykat.test$prediction$cell.names)
+    seu$newB.copykat.pred <- copykat.test$prediction$copykat.pred[idx]
+    saveRDS(seu, file = file.path(out_loc,"results/rds",paste0(ind.lib,".rds")))
+  }
+}
+
+project_root  <- rprojroot::find_root(rprojroot::is_git_root)
+projectID <- "SCPCP000003"
+out_loc <- file.path(project_root, "analyses/cell-type-nonETP-ALL-03")
+data_loc <- file.path(project_root, "data/current",projectID)
+setwd(file.path(out_loc,"results/copykat_output"))
+
+metadata <- read.table(file.path(data_loc,"single_cell_metadata.tsv"), sep = "\t", header = T)
+metadata <- metadata[which(metadata$scpca_project_id == projectID &
+                             metadata$diagnosis == "Non-early T-cell precursor T-cell acute lymphoblastic leukemia"), ]
+libraryID <- metadata$scpca_library_id
+
+purrr::walk(libraryID, run_copykat)
diff --git a/analyses/cell-type-nonETP-ALL-03/scripts/exploratory-analyses/00-make-gene-order-file.R b/analyses/cell-type-nonETP-ALL-03/scripts/exploratory-analyses/00-make-gene-order-file.R
new file mode 100644
index 000000000..1c04ff91e
--- /dev/null
+++ b/analyses/cell-type-nonETP-ALL-03/scripts/exploratory-analyses/00-make-gene-order-file.R
@@ -0,0 +1,58 @@
+#!/usr/bin/env Rscript
+
+project_root  <- rprojroot::find_root(rprojroot::is_git_root)
+
+library(optparse)
+
+option_list <- list(
+  make_option(
+    opt_str = c("--gtf_file"),
+    type = "character",
+    default = "s3://scpca-references/homo_sapiens/ensembl-104/annotation/Homo_sapiens.GRCh38.104.gtf.gz",
+    help = "URI to gtf file to create gene order file."
+  ),
+  make_option(
+    opt_str = c("--local_ref_dir"),
+    type = "character",
+    default = file.path(project_root, "references", "infercnv_refs"),
+    help = "Directory to use for saving GTF file and gene order file."
+  ),
+  make_option(
+    opt_str = c("--scratch_dir"),
+    type = "character",
+    default = file.path(project_root, "scratch"),
+    help = "Path to store copied GTF file"
+  )
+)
+
+# Parse options
+opt <- parse_args(OptionParser(option_list = option_list))
+
+# create ref directory if doesn't already exist
+fs::dir_create(opt$local_ref_dir)
+
+# sync gtf file to local directory
+gtf_filename <- basename(opt$gtf_file)
+
+local_gtf_file <- file.path(opt$scratch_dir, gtf_filename)
+if (!file.exists(local_gtf_file)) {
+  sync_call <- glue::glue("aws s3 cp {opt$gtf_file} {local_gtf_file} --no-sign-request")
+  system(sync_call)
+}
+
+# define gene order file name using gtf file
+gtf_basename <- stringr::str_remove(gtf_filename, ".gtf.gz")
+gene_order_filename <- glue::glue("{gtf_basename}.gene_order.txt")
+gene_order_file <- file.path(opt$local_ref_dir, gene_order_filename)
+
+# read in gtf file
+gtf <- rtracklayer::import(local_gtf_file, feature.type = "gene")
+
+# format gene order file
+gtf_df <- gtf |>
+  as.data.frame() |>
+  dplyr::select(gene_id, seqnames, start, end) |>
+  dplyr::mutate(seqnames = glue::glue("chr{seqnames}"))
+
+# export gene order file
+readr::write_tsv(gtf_df, gene_order_file, col_names = FALSE)
diff --git a/analyses/cell-type-nonETP-ALL-03/scripts/exploratory-analyses/copykat_exploration.R b/analyses/cell-type-nonETP-ALL-03/scripts/exploratory-analyses/copykat_exploration.R
index 89ef14248..92e4ccdac 100644
--- a/analyses/cell-type-nonETP-ALL-03/scripts/exploratory-analyses/copykat_exploration.R
+++ b/analyses/cell-type-nonETP-ALL-03/scripts/exploratory-analyses/copykat_exploration.R
@@ -8,31 +8,31 @@ library(dplyr)
 
 copykatInterpret <- function(annot.obj, library.id, ct.colors){
   tryCatch({
-    exprs <- data.frame(FetchData(annot.obj, vars = c("sctype_classification","copykat.pred","lowConfidence_annot")))
+    exprs <- data.frame(FetchData(annot.obj, vars = c("sctype_classification","newB.copykat.pred","lowConfidence_annot")))
     df <- exprs %>%
-      group_by(copykat.pred, sctype_classification) %>%
+      group_by(newB.copykat.pred, sctype_classification) %>%
       count(name = "Frequency")
     total_df <- df %>%
-      group_by(copykat.pred) %>%
+      group_by(newB.copykat.pred) %>%
       summarise(Total = sum(Frequency))
     p1 <- ggplot() +
-      geom_bar(data = df, aes(x = copykat.pred, y = Frequency, fill =  sctype_classification), width = 0.5, stat = "identity", position = "fill") +
-      geom_text(data = total_df, aes(y = 100, x = copykat.pred, label = Total), size = 4, position = position_fill(vjust = 1.02)) +
+      geom_bar(data = df, aes(x = newB.copykat.pred, y = Frequency, fill =  sctype_classification), width = 0.5, stat = "identity", position = "fill") +
+      geom_text(data = total_df, aes(y = 100, x = newB.copykat.pred, label = Total), size = 4, position = position_fill(vjust = 1.02)) +
       scale_fill_manual(values = ct_color)
     
     df <- exprs %>%
-      dplyr::group_by(copykat.pred, lowConfidence_annot) %>%
+      dplyr::group_by(newB.copykat.pred, lowConfidence_annot) %>%
       dplyr::count(name = "Frequency")
     p2 <- ggplot() + 
-      geom_bar(data = df, aes(x = copykat.pred, y = Frequency, fill =  lowConfidence_annot), width = 0.5, stat = "identity", position = "fill") +
-      geom_text(data = total_df, aes(y = 100, x = copykat.pred, label = Total), size = 4, position = position_fill(vjust = 1.02)) + 
+      geom_bar(data = df, aes(x = newB.copykat.pred, y = Frequency, fill =  lowConfidence_annot), width = 0.5, stat = "identity", position = "fill") +
+      geom_text(data = total_df, aes(y = 100, x = newB.copykat.pred, label = Total), size = 4, position = position_fill(vjust = 1.02)) + 
       scale_fill_manual(values = ct_color)
     cowplot::plot_grid(plotlist = list(p1,p2), nrow = 1) + 
       cowplot::draw_figure_label(library.id, position = "top", size = 14, fontface = "bold")
     ggsave(file.path(out_loc,"plots/copykat_exploration",paste0(library.id,"_celltypeVScopykat.png")), width = 10, height = 5, bg = "white", dpi = 150)
     
     ### plotting blast module scores 
-    Idents(annot.obj) <- factor(annot.obj$copykat.pred, levels = c("aneuploid","diploid","not.defined")) 
+    Idents(annot.obj) <- factor(annot.obj$newB.copykat.pred, levels = c("aneuploid","diploid","not.defined")) 
     VlnPlot(annot.obj, features = "Blast_Features1") + ggtitle(paste0(library.id,": Blast module score")) + NoLegend()
     ggsave(file.path(out_loc,"plots/copykat_exploration",paste0(library.id,"_blastModuleScore.png")), width = 6, height = 6, bg = "white", dpi = 150)
   }, error=function(e){})
diff --git a/analyses/cell-type-nonETP-ALL-03/scripts/exploratory-analyses/run_infercnv.R b/analyses/cell-type-nonETP-ALL-03/scripts/exploratory-analyses/run_infercnv.R
new file mode 100644
index 000000000..68ab32063
--- /dev/null
+++ b/analyses/cell-type-nonETP-ALL-03/scripts/exploratory-analyses/run_infercnv.R
@@ -0,0 +1,52 @@
+#!/usr/bin/env Rscript
+
+#sudo apt-get install r-cran-rjags
+#This script runs inferCNV using the new B cells, and trying to identify "non-malignant" group based on the infercnv.png
+
+library(Seurat)
+
+run_inferCNV <- function(ind.lib){
+  dir.create(file.path(scratch_dir, ind.lib), showWarnings = FALSE)
+  seu <- readRDS(file.path(out_loc,"results/rds",paste0(ind.lib,".rds")))
+  annot.file <- file.path(out_loc,"results",paste0(ind.lib,"_newB-normal-annotation.txt"))
+  infercnv_obj <- infercnv::CreateInfercnvObject(raw_counts_matrix=seu@assays[["RNA"]]@counts,
+                                                 annotations_file=annot.file,
+                                                 delim="\t",
+                                                 gene_order_file=geneFile,
+                                                 ref_group_names="new B") 
+  options(scipen = 100)
+  infercnv_obj <- infercnv::run(infercnv_obj,
+                                cutoff = 0.1, # use 1 for smart-seq, 0.1 for 10x-genomics
+                                out_dir = file.path(scratch_dir,ind.lib), # save all intermediate files to scratch dir
+                                denoise = T, HMM = T, analysis_mode = "samples",
+                                save_rds = F, # don't save the intermediate rds files
+                                num_threads = parallel::detectCores() - 1)
+  
+  # create table with barcodes and CNVs for each chromosome
+  infercnv::add_to_seurat(
+    seurat_obj = NULL,
+    infercnv_output_path = file.path(scratch_dir, ind.lib))
+  
+  ### adding clusterID from the cutting of hierarchical clustering to seu object
+  final_cnv_obj <- readRDS(file.path(out_loc, "results/infercnv_output", paste0(ind.lib,"_run.final.infercnv_obj")))
+  hres <- final_cnv_obj@tumor_subclusters$hc$all_observations
+  obs.clusID <- cutree(hres,4) #4 clusters for SCPCL000703
+  hres <- dendextend::color_branches(hres, k= 4) 
+  plot(hres)
+  seu$infercnv.pred <- obs.clusID[match(names(obs.clusID), colnames(seu))]
+}
+
+project_root  <- rprojroot::find_root(rprojroot::is_git_root)
+projectID <- "SCPCP000003"
+out_loc <- file.path(project_root, "analyses/cell-type-nonETP-ALL-03")
+data_loc <- file.path(project_root, "data/current",projectID)
+scratch_dir <- file.path(out_loc,"scratch")
+
+metadata <- read.table(file.path(data_loc,"single_cell_metadata.tsv"), sep = "\t", header = T)
+metadata <- metadata[which(metadata$scpca_project_id == projectID &
+                             metadata$diagnosis == "Non-early T-cell precursor T-cell acute lymphoblastic leukemia"), ]
+libraryID <- metadata$scpca_library_id
+
+geneFile <- file.path(project_root, "references/infercnv_refs/Homo_sapiens.GRCh38.104.gene_order.txt")
+
+purrr::walk(libraryID, run_inferCNV)
diff --git a/analyses/cell-type-nonETP-ALL-03/scripts/markerGenes_submission.R b/analyses/cell-type-nonETP-ALL-03/scripts/markerGenes_submission.R
new file mode 100644
index 000000000..ceb4283b0
--- /dev/null
+++ b/analyses/cell-type-nonETP-ALL-03/scripts/markerGenes_submission.R
@@ -0,0 +1,31 @@
+#!/usr/bin/env Rscript
+
+#This script converts the "Azimuth_BM_level1.csv" into the submissio format for marker genes
+
+project_root  <- rprojroot::find_root(rprojroot::is_git_root)
+projectID <- "SCPCP000003"
+out_loc <- file.path(project_root, "analyses/cell-type-nonETP-ALL-03")
+
+all_sources <- c("https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow",
+                 "doi:10.1038/s41598-023-39152-z","https://sctype.app/database.php")
+gene.df <- read.table(file.path(out_loc,"Azimuth_BM_level1.csv"), sep = ",", header = T)
+
+df1 <- c()
+for (i in 1:nrow(gene.df)){
+  tmp.gene <- strsplit(gene.df$ensembl_id_positive_marker[i],",")[[1]]
+  if (gene.df$cellName[i] == "Blast"){
+    source <- all_sources[2]
+  }else if (gene.df$cellName[i] %in% c("Pre Eryth","Cancer")){
+    source <- all_sources[3]
+  }else{source <- all_sources[1]}
+  
+  df1 <- rbind(df1,data.frame(ensembl_gene_id=tmp.gene,
+                              cell_type=rep(gene.df$cellName[i],length(tmp.gene)),
+                              source=rep(source,length(tmp.gene))))
+}
+
+df2 <- by(df1, df1$ensembl_gene_id, \(x) list2DF(lapply(x, \(.) toString(unique(.))))) |>
+  do.call(what=rbind)
+
+write.table(df2, file = file.path(out_loc,"submission_markerGenes.tsv"), sep = "\t", 
+            row.names = F, quote = F)
diff --git a/analyses/cell-type-nonETP-ALL-03/scripts/writeout_submission.R b/analyses/cell-type-nonETP-ALL-03/scripts/writeout_submission.R
new file mode 100644
index 000000000..dfb4a0173
--- /dev/null
+++ b/analyses/cell-type-nonETP-ALL-03/scripts/writeout_submission.R
@@ -0,0 +1,59 @@
+#!/usr/bin/env Rscript
+
+library(Seurat)
+library(ggplot2)
+
+writeout <- function(ind.lib, sample.ID, ct.colors, n.row = 1){
+  seu <- readRDS(file.path(out_loc,"results/rds",paste0(ind.lib,".rds")))
+  voi <- c('tumor_cell_classification','cell_type_assignment')
+  tumor_classification <- c('tumor','normal','unknown')
+  names(tumor_classification) <- c('aneuploid','diploid','not.defined')
+  seu$cell_type_assignment <- seu$sctype_classification
+  tryCatch({
+    seu$tumor_cell_classification <- as.vector(tumor_classification[match(seu$newB.copykat.pred,names(tumor_classification))])
+  }, error=function(e){})
+  tryCatch({
+    voi_df <- data.frame(FetchData(seu, vars = voi)) |> tibble::rownames_to_column(var = "cell_barcode")
+  }, error=function(e){})
+  final.df <- data.frame(scpca_sample_id=rep(sample.ID, nrow(voi_df)), voi_df,
+                         CL_ontology_id=gene.df$ontologyID[match(voi_df$cell_type_assignment,gene.df$cellName)])
+  write.table(final.df, sep = "\t", quote = F, row.names = F,
+              file = file.path(out_loc,"results/submission_table",paste0(ind.lib,"_metadata.tsv")))
+  
+  ## plotting the variables
+  plot.list <- list()
+  for (plot.type in voi){
+    if (plot.type == "cell_type_assignment"){
+      clrs <- ct.colors
+    } else{
+      clrs <- NULL
+    }
+    tryCatch({
+      plot.list[[plot.type]] <- DimPlot(seu, reduction = "Xumap_", group.by = plot.type, 
+                                        label = T, cols = clrs, repel = T) 
+    }, error=function(e){})
+  }
+  cowplot::plot_grid(plotlist = plot.list, nrow = n.row) + patchwork::plot_annotation(title = ind.lib) &  
+    theme(plot.title = element_text(hjust = 0.5, size = 18, face="bold")) 
+  ggsave(file.path(out_loc,"results/submission_table",paste0("multipanels_",ind.lib,".png")), width = 12, height = 5, bg = "white", dpi = 150)
+}
+
+project_root  <- rprojroot::find_root(rprojroot::is_git_root)
+projectID <- "SCPCP000003"
+out_loc <- file.path(project_root, "analyses/cell-type-nonETP-ALL-03")
+data_loc <- file.path(project_root, "data/current",projectID)
+dir.create(file.path(out_loc, "results/submission_table"), showWarnings = FALSE)
+
+gene.df <- read.table(file.path(out_loc, "Azimuth_BM_level1.csv"), sep = ",", header = T)
+ct_color <- c("darkorchid","skyblue2","dodgerblue2","gold","beige","sienna1","green4","navy",
+              "chocolate4","red","darkred","#6A3D9A","maroon","yellow4","grey35","black","lightpink","grey80")
+names(ct_color) <- c("B","CD4 T","CD8 T","DC","HSPC","Mono","NK","Other T","Macrophage",
+                     "Early Eryth","Late Eryth","Plasma","Platelet","Stromal","Blast","Cancer","Pre Eryth","Unknown")
+
+metadata <- read.table(file.path(data_loc,"single_cell_metadata.tsv"), sep = "\t", header = T)
+metadata <- metadata[which(metadata$scpca_project_id == projectID &
+                             metadata$diagnosis == "Non-early T-cell precursor T-cell acute lymphoblastic leukemia"), ]
+libraryID <- metadata$scpca_library_id
+sampleID <- metadata$scpca_sample_id
+
+purrr::walk2(libraryID, sampleID, ~ writeout(ind.lib = .x, sample.ID = .y, ct.colors = ct_color))
diff --git a/analyses/cell-type-nonETP-ALL-03/submission_markerGenes.tsv b/analyses/cell-type-nonETP-ALL-03/submission_markerGenes.tsv
new file mode 100644
index 000000000..bf66d938e
--- /dev/null
+++ b/analyses/cell-type-nonETP-ALL-03/submission_markerGenes.tsv
@@ -0,0 +1,152 @@
+ensembl_gene_id	cell_type	source
+ENSG00000002586	Blast	doi:10.1038/s41598-023-39152-z
+ENSG00000005961	Early Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000007062	Cancer	https://sctype.app/database.php
+ENSG00000011465	Stromal	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000012124	B	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000014914	Mono	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000026508	Cancer	https://sctype.app/database.php
+ENSG00000041982	Stromal	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000047457	Stromal	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000048462	Plasma	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000069667	Other T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000070031	DC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000072274	Pre Eryth	https://sctype.app/database.php
+ENSG00000073754	Macrophage	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000075340	Late Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000075618	Early Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000081059	CD4 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000081237	Pre Eryth	https://sctype.app/database.php
+ENSG00000086205	Cancer	https://sctype.app/database.php
+ENSG00000088726	Platelet	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000091513	Stromal	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000100385	NK	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000100450	CD8 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000101200	HSPC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000102145	Early Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000104660	CD4 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000104894	B	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000104974	Mono	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000105251	DC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000105369	B	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000105610	Early Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000106327	Early Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000107742	Other T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000110195	Pre Eryth	https://sctype.app/database.php
+ENSG00000110203	Mono	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000111057	Cancer	https://sctype.app/database.php
+ENSG00000111796	Other T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000112077	HSPC, Late Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000112175	Stromal	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000112212	Late Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000113088	Other T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000113140	Platelet	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000115232	Pre Eryth	https://sctype.app/database.php
+ENSG00000115461	Stromal	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000115607	NK	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000115718	DC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000115884	Plasma	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000116191	B	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000117281	NK	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000117632	Blast	doi:10.1038/s41598-023-39152-z
+ENSG00000119865	Early Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000119888	HSPC, Late Eryth, Cancer	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow, https://sctype.app/database.php
+ENSG00000121769	Macrophage	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000123416	Blast	doi:10.1038/s41598-023-39152-z
+ENSG00000124491	Platelet	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000124766	Blast	doi:10.1038/s41598-023-39152-z
+ENSG00000125810	Mono	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000130203	Macrophage	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000130208	Early Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000131016	HSPC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000132514	DC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000132704	B	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000133742	Pre Eryth	https://sctype.app/database.php
+ENSG00000133789	B	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000134545	NK	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000135218	Pre Eryth	https://sctype.app/database.php
+ENSG00000135525	Early Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000138639	B	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000138795	CD4 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000139193	CD4 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000139329	Stromal	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000141736	Cancer	https://sctype.app/database.php
+ENSG00000143184	NK	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000143297	Plasma	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000144290	Other T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000145220	Other T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000147571	Stromal	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000150045	NK	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000150681	Platelet	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000150687	NK	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000152518	Other T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000152583	Stromal	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000153064	B	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000153071	Platelet	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000153563	CD8 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000155367	DC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000156738	B	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000156966	NK	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000158825	Mono	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000159189	Macrophage	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000160307	CD8 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000160654	CD4 T, CD8 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000162444	Mono	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000163534	B	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000163554	HSPC, Late Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000163687	DC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000163736	Platelet	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000163737	Platelet	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000164692	Stromal	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000166211	Macrophage	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000166523	Mono	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000167286	CD4 T, CD8 T, Blast	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow, doi:10.1038/s41598-023-39152-z
+ENSG00000167476	Plasma	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000168685	CD4 T, Other T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000168913	DC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000169432	DC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000169704	Platelet	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000170180	Pre Eryth	https://sctype.app/database.php
+ENSG00000170323	Macrophage	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000170891	HSPC, Early Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000171051	Mono	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000172005	CD4 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000172116	CD8 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000172247	HSPC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000172995	HSPC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000173369	Macrophage	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000173372	Macrophage	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000173762	Blast	doi:10.1038/s41598-023-39152-z
+ENSG00000175792	Pre Eryth	https://sctype.app/database.php
+ENSG00000176783	Platelet	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000177606	Blast	doi:10.1038/s41598-023-39152-z
+ENSG00000178573	Other T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000179348	Early Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000184613	CD8 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000186074	Mono	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000186710	HSPC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000187699	Platelet	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000188672	HSPC, Late Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000189430	NK	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000196188	Late Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000197353	Mono	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000198178	DC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000198574	NK	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000198851	CD4 T, CD8 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000204010	Late Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000211640	Plasma	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000211673	Plasma	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000211685	Plasma	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000213934	Late Eryth	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000215788	Other T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000222037	Plasma	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000223609	Pre Eryth	https://sctype.app/database.php
+ENSG00000227191	CD8 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000227507	CD4 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000239961	DC	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000240505	Plasma	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000243466	Plasma	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000244734	Pre Eryth	https://sctype.app/database.php
+ENSG00000250722	Macrophage	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000271503	CD8 T	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow
+ENSG00000275385	Macrophage	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow