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bin
bin
 
 
control
control
 
 
data
data
 
 
knit
knit
 
 
sample_info
sample_info
 
 
singularity
singularity
 
 
src
src
 
 
2019-01-04-cluster-names.txt
2019-01-04-cluster-names.txt
 
 
FigS15-interactive.html
FigS15-interactive.html
 
 
Makefile
Makefile
 
 
README.md
README.md
 
 
arl15-snp.bed
arl15-snp.bed
 
 
arl15.bed
arl15.bed
 
 
arl15peak.bed
arl15peak.bed
 
 
atac-allelic-bias-by-cell-type.nf
atac-allelic-bias-by-cell-type.nf
 
 
atac-correlation.nf
atac-correlation.nf
 
 
atac.nextflow.config
atac.nextflow.config
 
 
check-meuleman-snp-overlap.R
check-meuleman-snp-overlap.R
 
 
chromvar.nf
chromvar.nf
 
 
cicero-no-binarize.nf
cicero-no-binarize.nf
 
 
cicero-snps.bed
cicero-snps.bed
 
 
cluster-names.txt
cluster-names.txt
 
 
counts.nf
counts.nf
 
 
delta-svm-diamante-loci.nf
delta-svm-diamante-loci.nf
 
 
deltasvm-config.nf
deltasvm-config.nf
 
 
determine-species-dual-modality.nf
determine-species-dual-modality.nf
 
 
fimo.nf
fimo.nf
 
 
find-disrupted-motifs.nf
find-disrupted-motifs.nf
 
 
find-rat-snp.nf
find-rat-snp.nf
 
 
fragment-counts-atac.nf
fragment-counts-atac.nf
 
 
gkmexplain-and-fimo-new-plots.nf
gkmexplain-and-fimo-new-plots.nf
 
 
hic.nf
hic.nf
 
 
initial-thresholds-atac.txt
initial-thresholds-atac.txt
 
 
initial-thresholds-rna.txt
initial-thresholds-rna.txt
 
 
itpr2-snp.bed
itpr2-snp.bed
 
 
itpr2.bed
itpr2.bed
 
 
ldsc-T2D-joint-model.nf
ldsc-T2D-joint-model.nf
 
 
ldsc-T2D-one-model-per-cell-type.nf
ldsc-T2D-one-model-per-cell-type.nf
 
 
ldsc-UKB-new-baseline.nf
ldsc-UKB-new-baseline.nf
 
 
ldsc-annotations.csv
ldsc-annotations.csv
 
 
ldsc-update-baseline-model-min-maf.nf
ldsc-update-baseline-model-min-maf.nf
 
 
library-labels.txt
library-labels.txt
 
 
liger-human-and-rat-with-lambda.nf
liger-human-and-rat-with-lambda.nf
 
 
logistic-regression.nf
logistic-regression.nf
 
 
make-quality-nuclei-count-files.nf
make-quality-nuclei-count-files.nf
 
 
make-read-beds.nf
make-read-beds.nf
 
 
make-rna-qc.nf
make-rna-qc.nf
 
 
make-tables.nf
make-tables.nf
 
 
make-wasp-input-bams.nf
make-wasp-input-bams.nf
 
 
manuscript-figures-v2.nf
manuscript-figures-v2.nf
 
 
nextflow.config
nextflow.config
 
 
prep-meuleman-with-hesc.nf
prep-meuleman-with-hesc.nf
 
 
process-by-cluster.nf
process-by-cluster.nf
 
 
process-snATAC-as-bulk.nf
process-snATAC-as-bulk.nf
 
 
qc.nf
qc.nf
 
 
rat-arl15-snp.bed
rat-arl15-snp.bed
 
 
reformat-ukbb.nf
reformat-ukbb.nf
 
 
rna.nextflow.config
rna.nextflow.config
 
 
rs227731-hg19.bed
rs227731-hg19.bed
 
 
rs227731-hg38.bed
rs227731-hg38.bed
 
 
rs227731-overlap.sh
rs227731-overlap.sh
 
 
seurat-2.nf
seurat-2.nf
 
 
signac-link-peaks-to-genes-across-clusters-flexible.nf
signac-link-peaks-to-genes-across-clusters-flexible.nf
 
 
snp-roadmap-chromhmm-state.nf
snp-roadmap-chromhmm-state.nf
 
 
snps-for-manuscript.txt
snps-for-manuscript.txt
 
 
starch-bdg.nf
starch-bdg.nf
 
 
ukb-traits.txt
ukb-traits.txt
 
 
zenodo-noreads-readme.txt
zenodo-noreads-readme.txt
 
 
zenodo-readme.txt
zenodo-readme.txt
 
 
zenodo-reads-readme.txt
zenodo-reads-readme.txt
 
 
zenodo-sample-info.txt
zenodo-sample-info.txt
 
 

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Single-nuclei muscle project

Code for manuscript 'Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits'

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  • HTML 72.6%
  • Shell 10.7%
  • Python 9.5%
  • Nextflow 2.6%
  • R 2.4%
  • Makefile 1.1%
  • Other 1.1%