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added marker genes table in final submission format
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analyses/cell-type-nonETP-ALL-03/scripts/markerGenes_submission.R
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| #!/usr/bin/env Rscript | ||
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| #This script converts the "Azimuth_BM_level1.csv" into the submissio format for marker genes | ||
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| project_root <- rprojroot::find_root(rprojroot::is_git_root) | ||
| projectID <- "SCPCP000003" | ||
| out_loc <- file.path(project_root, "analyses/cell-type-nonETP-ALL-03") | ||
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| 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) | ||
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| 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$cellName[i] %in% c("Pre Eryth","Cancer")){ | ||
| source <- all_sources[3] | ||
| }else{source <- all_sources[1]} | ||
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| df1 <- rbind(df1,data.frame(ensembl_gene_id=tmp.gene, | ||
| cell_type=rep(gene.df$cellName[i],length(tmp.gene)), | ||
| source=rep(source,length(tmp.gene)))) | ||
| } | ||
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| df2 <- by(df1, df1$ensembl_gene_id, \(x) list2DF(lapply(x, \(.) toString(unique(.))))) |> | ||
| do.call(what=rbind) | ||
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| write.table(df2, file = file.path(out_loc,"submission_markerGenes.tsv"), sep = "\t", | ||
| row.names = F, quote = F) |
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analyses/cell-type-nonETP-ALL-03/submission_markerGenes.tsv
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| 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 |