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_bookdown_files/SCmultiomics_longCOVID_files	_bookdown_files/SCmultiomics_longCOVID_files
docs	docs
images	images
.Rprofile	.Rprofile
.gitignore	.gitignore
00.cellranger-demultiplexing.Rmd	00.cellranger-demultiplexing.Rmd
01-data-loading.Rmd	01-data-loading.Rmd
02-donor-assignment.Rmd	02-donor-assignment.Rmd
03-rna-qc.Rmd	03-rna-qc.Rmd
04-atac-qc.Rmd	04-atac-qc.Rmd
05-merge-samples.Rmd	05-merge-samples.Rmd
06-rna-processing.Rmd	06-rna-processing.Rmd
07-confounding-factors.Rmd	07-confounding-factors.Rmd
08-atac-processing.Rmd	08-atac-processing.Rmd
09-batch-effects.Rmd	09-batch-effects.Rmd
10-SingleR.Rmd	10-SingleR.Rmd
11-rna-integration.Rmd	11-rna-integration.Rmd
12-atac-integration.Rmd	12-atac-integration.Rmd
13-cross-modal-integration.Rmd	13-cross-modal-integration.Rmd
14-marker-genes-identification.Rmd	14-marker-genes-identification.Rmd
15-peak-gene-linking.Rmd	15-peak-gene-linking.Rmd
16-motif-enrichment.Rmd	16-motif-enrichment.Rmd
17-chromvar-tf-activity.Rmd	17-chromvar-tf-activity.Rmd
18-gene-regulatory-networks.Rmd	18-gene-regulatory-networks.Rmd
19-regulon-activity-scoring.Rmd	19-regulon-activity-scoring.Rmd
20-tf-motif-marker-integration.Rmd	20-tf-motif-marker-integration.Rmd
21-pseudobulk-differential-expression.Rmd	21-pseudobulk-differential-expression.Rmd
README.md	README.md
SCmultiomics_longCOVID.Rmd	SCmultiomics_longCOVID.Rmd
SCmultiomics_longCOVID.Rproj	SCmultiomics_longCOVID.Rproj
SCmultiomics_longCOVID.html	SCmultiomics_longCOVID.html
_bookdown.yml	_bookdown.yml
_common.R	_common.R
_output.yml	_output.yml
book.bib	book.bib
creatingShinyCellModular.Rmd	creatingShinyCellModular.Rmd
index.Rmd	index.Rmd
notes.R	notes.R
packages.bib	packages.bib
preamble.tex	preamble.tex
pushgit.sh	pushgit.sh
renv.lock	renv.lock

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_bookdown_files/SCmultiomics_longCOVID_files

00.cellranger-demultiplexing.Rmd

01-data-loading.Rmd

02-donor-assignment.Rmd