Files in huqiwen0313/snarePip
snarePip
.coveragerc
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
Pipfile
R/QC.R
R/RcppExports.R
R/callPeaks.R
R/cicero.R
R/dm.R
R/doublet.R
R/linkage.R
R/motifs.R
R/processing.R
R/setObj.R
R/util.R
README.md
Snakefile.RNA
Snakefile.atac
conf/MT_gene.list
conf/R1_barcode_cfg
conf/R1_barcode_list_SNARE2
conf/R1_barcode_list_split-seq
conf/R1_dTN6_pairs.txt
conf/snareR.config.yaml
conf/split_seq.xml
conf/split_seq_barcodes
conf/whitelist
documentation/images/database.relationship.bmp
documentation/images/pipeline.figure.png
documentation/images/pipeline.module.overview.jpg
documentation/images/snarePip.dag.png
man/GetMarkerExprMatrix.Rd
man/PrepareFragmentPlot.Rd
man/RunJD.Rd
man/TSSenrichment.Rd
man/TSSenrichmentPlot.Rd
man/addAtacObj.Rd
man/addMotifMatrix.Rd
man/alignmentStat.Rd
man/assignPeakToGene.Rd
man/calDoubletScore.Rd
man/calJaccard.Rd
man/callMACs.Rd
man/callMACsCluster.Rd
man/cellStatistics.Rd
man/ciceroGeneActivity.Rd
man/createInputCDS.Rd
man/dimReduct.Rd
man/enrichMotifs.Rd
man/enrichMotifsDAR.Rd
man/fragmentOverlapPeaks.Rd
man/fragmentOverlapPeaksPlot.Rd
man/hvgPeaks.Rd
man/idenDAR.Rd
man/intPosMat.Rd
man/normJD.Rd
man/normPmatrix.Rd
man/plotAssoGenes.Rd
man/plotComponentVariancePagoda.Rd
man/plotDARoverlap.Rd
man/plotFeature.Rd
man/plotFragmentScatter.Rd
man/plotSaturation.Rd
man/plotSnareBarcodeComparison.Rd
man/plotTopMotifs.Rd
man/posMatrix.Rd
man/quickUmap.Rd
man/read.bam.tags.Rd
man/sampleBackgroundSeq.Rd
man/sampleCell.Rd
man/simulateDoubletMatrix.Rd
pytest.ini
rules/QC_atac.smk
rules/RNA_QC.smk
rules/RNA_fastqc.smk
rules/RNA_sample_level.smk
rules/atac_sampleLevel_QC.smk
rules/call_peaks_atac.smk
rules/drop_report.smk
rules/dropest_alignment.smk
rules/dual_omics.smk
rules/merge_dT_N6_barcode.smk
rules/merge_to_sampleLevel_atac.smk
rules/peakcalling_sampleLevel_atac.smk
rules/remove_contaminate.smk
rules/samtools_atac.smk
rules/sinto_atac.smk
rules/snapTag_atac.smk
rules/snap_pre.smk
rules/snaptools_align.smk
scripts/ATAC.report.experiment.level.html.rmd
scripts/RNA.explevel.QC.R
scripts/RNA.report.Rmd
scripts/RNA.sample.QC.R
scripts/addLibID_generate_seurat_dropest_d.r
scripts/collapseBarcodesBam.pl
scripts/distr.sample.R
scripts/dropReport_lib_one.Rsc
scripts/dual.omics.report.rmd
scripts/enumerate_mm_edit.pl
scripts/generate.QC.report.3.R
scripts/get_barcodes_by_pos_SNARE2.pl
scripts/sampleLevel.peakCalling.R
scripts/sampleLevelQC.2.R
setup.py
snarePip.Rproj
snarePip/__init__.py
snarePip/__main__.py
snarePip/cli.py
snarePip/io.py
snarePip/luigi/__init__.py
snarePip/luigi/dask/__init__.py
snarePip/luigi/dask/target.py
snarePip/luigi/task.py
snarePip/tasks/__init__.py
snarePip/tasks/metable.py
snarePip/tasks/qc.py
snarePip/tasks/snakemakeRun.py
snarePip/tasks/upload.py
src/basic.manipulation.cpp
test_pset.py
