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'

Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
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

porchard/2021-03-sn-muscle

Folders and files

Latest commit

History