Files in hbc/bcbioRNASeq

Bcbio RNA-Seq

.Rbuildignore

.gitignore

.lintr

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/AllClasses.R R/AllGenerators.R R/AllGenerics.R R/AllGlobals.R R/coerce-methods.R R/counts-methods.R R/data.R R/deprecated.R R/extract-methods.R R/internal-assert.R R/internal-deseq2.R R/internal-featurecounts.R R/internal-ggplot2.R R/internal-tximport.R R/package.R R/plot5Prime3PrimeBias-methods.R R/plotCorrelationHeatmap-methods.R R/plotCounts-methods.R R/plotCountsPerBiotype-methods.R R/plotCountsPerFeature-methods.R R/plotDispEsts-methods.R R/plotExonicMappingRate-methods.R R/plotFeatureSaturation-methods.R R/plotGenderMarkers-methods.R R/plotIntronicMappingRate-methods.R R/plotMappedReads-methods.R R/plotMappingRate-methods.R R/plotMeanSd-methods.R R/plotPca-methods.R R/plotPcaCovariates-methods.R R/plotPseudoVsAlignedCounts-methods.R R/plotQc-methods.R R/plotRrnaMappingRate-methods.R R/plotTotalReads-methods.R R/reexports.R R/relativeLogExpression-methods.R R/show-methods.R R/slotAlignedCounts-methods.R R/tmm-methods.R R/updateObject-methods.R README.md

_pkgdown.yml

data-raw/.gitignore

data-raw/bcb.R

data/bcb.rda

inst/CITATION

inst/extdata/bcbio/2018-03-18_GSE65267-merged/bcbio-nextgen-commands.log

inst/extdata/bcbio/2018-03-18_GSE65267-merged/bcbio-nextgen.log

inst/extdata/bcbio/2018-03-18_GSE65267-merged/combined.counts

inst/extdata/bcbio/2018-03-18_GSE65267-merged/programs.txt

inst/extdata/bcbio/2018-03-18_GSE65267-merged/project-summary.yaml

inst/extdata/bcbio/2018-03-18_GSE65267-merged/tx2gene.csv

inst/extdata/bcbio/control_rep1/salmon/quant.sf

inst/extdata/bcbio/control_rep2/salmon/quant.sf

inst/extdata/bcbio/control_rep3/salmon/quant.sf

inst/extdata/bcbio/fa_day7_rep1/salmon/quant.sf

inst/extdata/bcbio/fa_day7_rep2/salmon/quant.sf

inst/extdata/bcbio/fa_day7_rep3/salmon/quant.sf

inst/extdata/bcbio/sample_metadata.csv

inst/rmarkdown/templates/01-quality-control/skeleton/skeleton.Rmd

inst/rmarkdown/templates/01-quality-control/template.yaml

inst/rmarkdown/templates/02-differential-expression/skeleton/skeleton.Rmd

inst/rmarkdown/templates/02-differential-expression/template.yaml

inst/rmarkdown/templates/03-functional-analysis/skeleton/.gitignore

inst/rmarkdown/templates/03-functional-analysis/skeleton/skeleton.Rmd

inst/rmarkdown/templates/03-functional-analysis/template.yaml

longtests/testthat.R longtests/testthat/test-bcbioRNASeq.R longtests/testthat/test-f1000v2.R man/bcb.Rd man/bcbioRNASeq-class.Rd man/bcbioRNASeq-package.Rd man/bcbioRNASeq.Rd man/bcbioRNASeqTestsURL.Rd man/bcbioRnaSeqTestsUrl.Rd man/coerce.Rd man/counts.Rd man/deprecated.Rd man/extract.Rd man/plot5Prime3PrimeBias.Rd man/plotCorrelationHeatmap.Rd man/plotCounts.Rd man/plotCountsPerBiotype.Rd man/plotCountsPerFeature.Rd man/plotDispEsts.Rd man/plotExonicMappingRate.Rd man/plotFeatureSaturation.Rd man/plotGenderMarkers.Rd man/plotIntronicMappingRate.Rd man/plotMappedReads.Rd man/plotMappingRate.Rd man/plotMeanSd.Rd man/plotPca.Rd man/plotPcaCovariates.Rd man/plotPseudoVsAlignedCounts.Rd man/plotQc.Rd man/plotRrnaMappingRate.Rd man/plotTotalReads.Rd man/reexports.Rd man/relativeLogExpression.Rd man/show.Rd man/slotAlignedCounts.Rd man/tmm.Rd man/updateObject.Rd

package.Rproj

pkgdown/extra.css

tests/testthat.R

tests/testthat/.gitignore

tests/testthat/helper-cache.R tests/testthat/helper-globals.R tests/testthat/test-bcb.R tests/testthat/test-bcbioRNASeq.R tests/testthat/test-coerce.R tests/testthat/test-counts.R tests/testthat/test-extract.R tests/testthat/test-plotCorrelationHeatmap.R tests/testthat/test-plotCounts.R tests/testthat/test-plotCountsPerBiotype.R tests/testthat/test-plotCountsPerFeature.R tests/testthat/test-plotDispEsts.R tests/testthat/test-plotFeatureSaturation.R tests/testthat/test-plotFeaturesDetected.R tests/testthat/test-plotGenderMarkers.R tests/testthat/test-plotHeatmap.R tests/testthat/test-plotMeanSd.R tests/testthat/test-plotPca.R tests/testthat/test-plotPcaCovariates.R tests/testthat/test-plotPseudoVsAlignedCounts.R tests/testthat/test-plotQc.R tests/testthat/test-relativeLogExpression.R tests/testthat/test-sampleData.R tests/testthat/test-show.R tests/testthat/test-slotAlignedCounts.R tests/testthat/test-tmm.R tests/testthat/test-updateObject.R

todo.org

vignettes/.gitignore

vignettes/bcbiornaseq.Rmd

hbc/bcbioRNASeq documentation built on March 28, 2024, 3:01 p.m.