Files in lcolladotor/derfinder
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
.Rbuildignore
.github/.gitignore
.github/CODE_OF_CONDUCT.md
.github/CONTRIBUTING.md
.github/ISSUE_TEMPLATE/feature_request_template.md
.github/ISSUE_TEMPLATE/issue_template.md
.github/SUPPORT.md
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/Deprecated.R
R/analyzeChr.R
R/annotateRegions.R
R/calculatePvalues.R
R/calculateStats.R
R/coerceGR.R
R/collapseFullCoverage.R
R/coverageToExon.R
R/createBw.R
R/createBwSample.R
R/define_cluster.R
R/derfinder-package.R
R/extendedMapSeqlevels.R
R/filterData.R
R/findRegions.R
R/fullCoverage.R
R/genomeData-data.R
R/genomeDataRaw-data.R
R/genomeFstats-data.R
R/genomeInfo-data.R
R/genomeRegions-data.R
R/genomicState-data.R
R/getRegionCoverage.R
R/getTotalMapped.R
R/loadCoverage.R
R/makeGenomicState.R
R/makeModels.R
R/mergeResults.R
R/preprocessCoverage.R
R/railMatrix.R
R/rawFiles.R
R/regionMatrix.R
R/sampleDepth.R
R/utils.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
data/genomeData.RData
data/genomeDataRaw.RData
data/genomeFstats.RData
data/genomeInfo.RData
data/genomeRegions.RData
data/genomicState.RData
derfinder.Rproj
dev/01_create_pkg.R
dev/02_git_github_setup.R
dev/03_core_files.R
dev/04_update.R
inst/CITATION
inst/extdata/chr21/annotation.Rdata
inst/extdata/chr21/coveragePrep.Rdata
inst/extdata/chr21/fstats.Rdata
inst/extdata/chr21/optionsStats.Rdata
inst/extdata/chr21/regions.Rdata
inst/extdata/chr21/timeinfo.Rdata
inst/extdata/genomeData/ERR009101_accepted_hits.bam
inst/extdata/genomeData/ERR009101_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009102_accepted_hits.bam
inst/extdata/genomeData/ERR009102_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009105_accepted_hits.bam
inst/extdata/genomeData/ERR009105_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009107_accepted_hits.bam
inst/extdata/genomeData/ERR009107_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009108_accepted_hits.bam
inst/extdata/genomeData/ERR009108_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009112_accepted_hits.bam
inst/extdata/genomeData/ERR009112_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009115_accepted_hits.bam
inst/extdata/genomeData/ERR009115_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009116_accepted_hits.bam
inst/extdata/genomeData/ERR009116_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009131_accepted_hits.bam
inst/extdata/genomeData/ERR009131_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009138_accepted_hits.bam
inst/extdata/genomeData/ERR009138_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009144_accepted_hits.bam
inst/extdata/genomeData/ERR009144_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009145_accepted_hits.bam
inst/extdata/genomeData/ERR009145_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009148_accepted_hits.bam
inst/extdata/genomeData/ERR009148_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009151_accepted_hits.bam
inst/extdata/genomeData/ERR009151_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009152_accepted_hits.bam
inst/extdata/genomeData/ERR009152_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009153_accepted_hits.bam
inst/extdata/genomeData/ERR009153_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009159_accepted_hits.bam
inst/extdata/genomeData/ERR009159_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009161_accepted_hits.bam
inst/extdata/genomeData/ERR009161_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009163_accepted_hits.bam
inst/extdata/genomeData/ERR009163_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009164_accepted_hits.bam
inst/extdata/genomeData/ERR009164_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009167_accepted_hits.bam
inst/extdata/genomeData/ERR009167_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031812_accepted_hits.bam
inst/extdata/genomeData/SRR031812_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031835_accepted_hits.bam
inst/extdata/genomeData/SRR031835_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031867_accepted_hits.bam
inst/extdata/genomeData/SRR031867_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031868_accepted_hits.bam
inst/extdata/genomeData/SRR031868_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031900_accepted_hits.bam
inst/extdata/genomeData/SRR031900_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031904_accepted_hits.bam
inst/extdata/genomeData/SRR031904_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031914_accepted_hits.bam
inst/extdata/genomeData/SRR031914_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031936_accepted_hits.bam
inst/extdata/genomeData/SRR031936_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031958_accepted_hits.bam
inst/extdata/genomeData/SRR031958_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031960_accepted_hits.bam
inst/extdata/genomeData/SRR031960_accepted_hits.bam.bai
man/analyzeChr.Rd
man/annotateRegions.Rd
man/calculatePvalues.Rd
man/calculateStats.Rd
man/coerceGR.Rd
man/collapseFullCoverage.Rd
man/coverageToExon.Rd
man/createBw.Rd
man/createBwSample.Rd
man/define_cluster.Rd
man/derfinder-deprecated.Rd
man/derfinder-package.Rd
man/extendedMapSeqlevels.Rd
man/filterData.Rd
man/findRegions.Rd
man/fullCoverage.Rd
man/genomeData.Rd
man/genomeDataRaw.Rd
man/genomeFstats.Rd
man/genomeInfo.Rd
man/genomeRegions.Rd
man/genomicState.Rd
man/getRegionCoverage.Rd
man/getTotalMapped.Rd
man/loadCoverage.Rd
man/makeGenomicState.Rd
man/makeModels.Rd
man/mergeResults.Rd
man/preprocessCoverage.Rd
man/railMatrix.Rd
man/rawFiles.Rd
man/regionMatrix.Rd
man/sampleDepth.Rd
pkgdown/extra.css
tests/test-all.R
tests/testthat/test-maxRegionGap.R
tests/testthat/test_ER_level.R
tests/testthat/test_Fstats.R
tests/testthat/test_annotation.R
tests/testthat/test_data.R
tests/testthat/test_findRegions.R
tests/testthat/test_misc.R
vignettes/derfinder-quickstart.Rmd
vignettes/derfinder-users-guide.Rmd
