Files in noush-joglekar/scisorseqr
Processes long reads for differential isoform analysis
.DS_Store
.Rbuildignore
.Rproj.user/7803476A/build_options
.Rproj.user/7803476A/console06/INDEX001
.Rproj.user/7803476A/sources/prop/6BAFA4AC
.Rproj.user/7803476A/sources/prop/88C8867F
.Rproj.user/7803476A/sources/prop/AA170670
.Rproj.user/7803476A/sources/prop/INDEX
.Rproj.user/shared/notebooks/patch-chunk-names
.Rproj.user/shared/notebooks/paths
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/DiffSplicingAnalysis.R
R/ExonQuant.R
R/FilterBCoutput.R
R/GO.Reference.R
R/GetBarcodes.R
R/InfoPerLongRead.R
R/IsoQuant.R
R/MMalign.R
R/MakeMatrices.R
R/MapAndFilter.R
R/STARalign.R
R/correctedBed2AllInfo.R
R/sigSplitPie.R
R/triHeatmap.R
R/utils-pipe.R
README.Rmd
README.md
inst/.DS_Store
inst/RScript/ExonCounting.R
inst/RScript/ExonTest.R
inst/RScript/GOAnalysisWithPlots.R
inst/RScript/IsoQuant.R
inst/RScript/IsoformTest.R
inst/RScript/PieChart_Viz.R
inst/RScript/triangleHeatmap_Viz.R
inst/WORDLIST
inst/bash/FilterBCReads.sh
inst/bash/STARcomm.sh
inst/bash/bed12_toAllInfo.sh
inst/bash/cagePolyA.sh
inst/bash/concat_ParallelizedBC.sh
inst/bash/exon.gtf.to.intron.gff3.awk
inst/bash/f2t.sh
inst/bash/isoQuant_ds.sh
inst/bash/longReadInfo.sh
inst/bash/mapAndAlignReads.sh
inst/bash/minimap2comm.sh
inst/bash/toolCheck.sh
inst/bash/v0.1.findNotAnnotatedStretches.awk
inst/bash/v0.1.getSpliceSiteSequence.awk
inst/bash/v1.0b.correct.strand.bySpliceSiteConsensus.awk
inst/bash/v1.0b.getGenes_andHighlightProblematicReadsAndGenes.awk
inst/bash/v2.1a.compareTranscriptEnds_vs_PolyAs.awk
inst/bash/v2.1a.compareTranscriptStarts_vs_CageTSS.awk
inst/extdata/ENSEMBLE_v21_ClearGeneNames
inst/extdata/gencode.vM21.annotation.gtf.gz
inst/extdata/userInput/FastqFiles/TestHipp.fastq.gz
inst/extdata/userInput/FastqFiles/TestPFC.fastq.gz
inst/extdata/userInput/bc_celltype_assignments
inst/extdata/userInput/condensedCellTypes
inst/extdata/userInput/config
inst/python/AllIsoformsXCell_sparseMatrix.py
inst/python/BarcodeDeconvolution.py
inst/python/Get_IsoformXClusterMat.py
inst/python/v0.2.executeInParallel.py
man/.DS_Store
man/DiffSplicingAnalysis.Rd
man/ExonQuant.Rd
man/FilterBCOutput.Rd
man/GO.Reference.Rd
man/GetBarcodes.Rd
man/InfoPerLongRead.Rd
man/IsoQuant.Rd
man/MMalign.Rd
man/MakeMatrices.Rd
man/MapAndFilter.Rd
man/STARalign.Rd
man/correctedBed2AllInfo.Rd
man/figures/.DS_Store
man/figures/README-flow-1.pdf
man/figures/README-flow-1.png
man/figures/README-flow-2.png
man/figures/condensedCellTypes.png
man/figures/examplePie.png
man/figures/scisorseqr.png
man/hello.Rd
man/pipe.Rd
man/sigSplitPie.Rd
man/triHeatmap.Rd
scisorseqr.Rproj
vignettes/.DS_Store
vignettes/.gitignore
vignettes/scisorseqr-StandardWorkflow.Rmd
vignettes/scisorseqr-StandardWorkflow.pdf
