Files in derfinder

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

NEWS.md

NAMESPACE

DESCRIPTION

README.md tests/test-all.R tests/testthat/test_ER_level.R tests/testthat/test-maxRegionGap.R tests/testthat/test_annotation.R tests/testthat/test_findRegions.R tests/testthat/test_misc.R tests/testthat/test_Fstats.R tests/testthat/test_data.R R/Deprecated.R R/coverageToExon.R R/regionMatrix.R R/utils.R R/extendedMapSeqlevels.R R/genomeFstats-data.R R/getRegionCoverage.R R/mergeResults.R R/filterData.R R/rawFiles.R R/sampleDepth.R R/preprocessCoverage.R R/makeGenomicState.R R/makeModels.R R/createBw.R R/fullCoverage.R R/calculateStats.R R/genomeDataRaw-data.R R/coerceGR.R R/findRegions.R R/genomeInfo-data.R R/analyzeChr.R R/collapseFullCoverage.R R/define_cluster.R R/genomeRegions-data.R R/railMatrix.R R/genomeData-data.R R/createBwSample.R R/getTotalMapped.R R/calculatePvalues.R R/annotateRegions.R R/genomicState-data.R R/derfinder-package.R R/loadCoverage.R man/derfinder-deprecated.Rd man/annotateRegions.Rd man/getTotalMapped.Rd man/createBw.Rd man/makeModels.Rd man/genomeRegions.Rd man/rawFiles.Rd man/genomeDataRaw.Rd man/analyzeChr.Rd man/railMatrix.Rd man/collapseFullCoverage.Rd man/mergeResults.Rd man/loadCoverage.Rd man/filterData.Rd man/createBwSample.Rd man/calculatePvalues.Rd man/findRegions.Rd man/getRegionCoverage.Rd man/genomeFstats.Rd man/makeGenomicState.Rd man/derfinder-package.Rd man/fullCoverage.Rd man/genomeData.Rd man/preprocessCoverage.Rd man/sampleDepth.Rd man/define_cluster.Rd man/coerceGR.Rd man/coverageToExon.Rd man/genomicState.Rd man/extendedMapSeqlevels.Rd man/calculateStats.Rd man/regionMatrix.Rd man/genomeInfo.Rd

inst/CITATION

inst/extdata/genomeData/SRR031835_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009131_accepted_hits.bam

inst/extdata/genomeData/SRR031812_accepted_hits.bam

inst/extdata/genomeData/ERR009153_accepted_hits.bam

inst/extdata/genomeData/ERR009116_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009148_accepted_hits.bam

inst/extdata/genomeData/SRR031812_accepted_hits.bam.bai

inst/extdata/genomeData/SRR031868_accepted_hits.bam

inst/extdata/genomeData/ERR009107_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009167_accepted_hits.bam.bai

inst/extdata/genomeData/SRR031936_accepted_hits.bam.bai

inst/extdata/genomeData/SRR031936_accepted_hits.bam

inst/extdata/genomeData/SRR031868_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009145_accepted_hits.bam.bai

inst/extdata/genomeData/SRR031900_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009152_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009161_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009101_accepted_hits.bam

inst/extdata/genomeData/ERR009151_accepted_hits.bam

inst/extdata/genomeData/ERR009144_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009115_accepted_hits.bam

inst/extdata/genomeData/ERR009163_accepted_hits.bam

inst/extdata/genomeData/ERR009159_accepted_hits.bam

inst/extdata/genomeData/ERR009164_accepted_hits.bam

inst/extdata/genomeData/ERR009112_accepted_hits.bam

inst/extdata/genomeData/SRR031960_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009105_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009151_accepted_hits.bam.bai

inst/extdata/genomeData/SRR031958_accepted_hits.bam.bai

inst/extdata/genomeData/SRR031914_accepted_hits.bam.bai

inst/extdata/genomeData/SRR031914_accepted_hits.bam

inst/extdata/genomeData/ERR009153_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009167_accepted_hits.bam

inst/extdata/genomeData/ERR009105_accepted_hits.bam

inst/extdata/genomeData/ERR009161_accepted_hits.bam

inst/extdata/genomeData/ERR009102_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009159_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009107_accepted_hits.bam

inst/extdata/genomeData/SRR031867_accepted_hits.bam

inst/extdata/genomeData/ERR009112_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009102_accepted_hits.bam

inst/extdata/genomeData/ERR009145_accepted_hits.bam

inst/extdata/genomeData/ERR009152_accepted_hits.bam

inst/extdata/genomeData/ERR009144_accepted_hits.bam

inst/extdata/genomeData/ERR009164_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009138_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009108_accepted_hits.bam

inst/extdata/genomeData/ERR009101_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009115_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009116_accepted_hits.bam

inst/extdata/genomeData/ERR009163_accepted_hits.bam.bai

inst/extdata/genomeData/SRR031900_accepted_hits.bam

inst/extdata/genomeData/ERR009131_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009108_accepted_hits.bam.bai

inst/extdata/genomeData/SRR031958_accepted_hits.bam

inst/extdata/genomeData/SRR031835_accepted_hits.bam

inst/extdata/genomeData/SRR031904_accepted_hits.bam

inst/extdata/genomeData/SRR031960_accepted_hits.bam

inst/extdata/genomeData/SRR031867_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009148_accepted_hits.bam.bai

inst/extdata/genomeData/SRR031904_accepted_hits.bam.bai

inst/extdata/genomeData/ERR009138_accepted_hits.bam

inst/extdata/chr21/optionsStats.Rdata

inst/extdata/chr21/fstats.Rdata

inst/extdata/chr21/regions.Rdata

inst/extdata/chr21/timeinfo.Rdata

inst/extdata/chr21/coveragePrep.Rdata

inst/extdata/chr21/annotation.Rdata

inst/doc/derfinder-quickstart.html

inst/doc/derfinder-users-guide.R

inst/doc/derfinder-users-guide.html

inst/doc/derfinder-quickstart.R inst/doc/derfinder-users-guide.Rmd inst/doc/derfinder-quickstart.Rmd

data/genomeInfo.RData

data/genomicState.RData

data/genomeFstats.RData

data/genomeData.RData

data/genomeRegions.RData

data/genomeDataRaw.RData

build/vignette.rds

vignettes/derfinder-users-guide.Rmd vignettes/derfinder-quickstart.Rmd

derfinder documentation built on Dec. 20, 2020, 2 a.m.