Files in hbc/bcbioRNASeq
RNA-Seq Utilities

.Rbuildignore
.gitignore
.lintr
.push.sh
.travis.yml
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/AllClasses.R R/AllGenerics.R R/bcbioRNASeq-package.R R/datasets.R R/deprecated.R R/internal-DESeq2.R R/internal-ggplot2.R R/internal-sampleDirs.R R/internal-tx2gene.R R/internal-tximport.R R/loadRNASeq.R R/methods-aggregateReplicates.R R/methods-alphaSummary.R R/methods-annotable.R R/methods-bcbio.R R/methods-colData.R R/methods-counts.R R/methods-design.R R/methods-flatFiles.R R/methods-gene2symbol.R R/methods-interestingGroups.R R/methods-meltLog10.R R/methods-metrics.R R/methods-plot53Bias.R R/methods-plotCorrelationHeatmap.R R/methods-plotCountDensity.R R/methods-plotCountsPerGene.R R/methods-plotDEGHeatmap.R R/methods-plotDispEsts.R R/methods-plotExonicMappingRate.R R/methods-plotGenderMarkers.R R/methods-plotGene.R R/methods-plotGeneSaturation.R R/methods-plotGenesDetected.R R/methods-plotHeatmap.R R/methods-plotIntronicMappingRate.R R/methods-plotMA.R R/methods-plotMappedReads.R R/methods-plotMappingRate.R R/methods-plotMeanSD.R R/methods-plotPCA.R R/methods-plotPCACovariates.R R/methods-plotRRNAMappingRate.R R/methods-plotTotalReads.R R/methods-plotVolcano.R R/methods-prepareRNASeqTemplate.R R/methods-resultsTables.R R/methods-sampleMetadata.R R/methods-subset.R R/methods-tmm.R R/methods-topTables.R R/methods-tpm.R R/onLoad.R R/reexports.R R/setAs.R README.md
_pkgdown.yml
bcbioRNASeq.Rproj
data-raw/examples.R data-raw/genderMarkers.R
data-raw/genderMarkers.xlsx
data/genderMarkers.rda
docs/LICENSE.html
docs/authors.html
docs/extra.css
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/reference/AllGenerics.html
docs/reference/aggregateReplicates.html
docs/reference/alphaSummary.html
docs/reference/annotable.html
docs/reference/bcbio.html
docs/reference/bcbioRNADataSet-class.html
docs/reference/bcbioRNASeq-class.html
docs/reference/bcbioRNASeq-package.html
docs/reference/bcbioRnaseq-package.html
docs/reference/coerce.html
docs/reference/colData.html
docs/reference/counts.html
docs/reference/deprecated.html
docs/reference/design.html
docs/reference/flatFiles.html
docs/reference/genderMarkers.html
docs/reference/gene2symbol.html
docs/reference/index.html
docs/reference/interestingGroups.html
docs/reference/loadRNASeq.html
docs/reference/meltLog10.html
docs/reference/metrics.html
docs/reference/plot53Bias-1.png
docs/reference/plot53Bias-2.png
docs/reference/plot53Bias-3.png
docs/reference/plot53Bias.html
docs/reference/plotCorrelationHeatmap-1.png
docs/reference/plotCorrelationHeatmap-2.png
docs/reference/plotCorrelationHeatmap-3.png
docs/reference/plotCorrelationHeatmap-4.png
docs/reference/plotCorrelationHeatmap.html
docs/reference/plotCountDensity-1.png
docs/reference/plotCountDensity-2.png
docs/reference/plotCountDensity-3.png
docs/reference/plotCountDensity.html
docs/reference/plotCountsPerGene-1.png
docs/reference/plotCountsPerGene-2.png
docs/reference/plotCountsPerGene-3.png
docs/reference/plotCountsPerGene.html
docs/reference/plotDEGHeatmap-1.png
docs/reference/plotDEGHeatmap-2.png
docs/reference/plotDEGHeatmap.html
docs/reference/plotDispEsts-1.png
docs/reference/plotDispEsts-2.png
docs/reference/plotDispEsts.html
docs/reference/plotExonicMappingRate-1.png
docs/reference/plotExonicMappingRate-2.png
docs/reference/plotExonicMappingRate-3.png
docs/reference/plotExonicMappingRate.html
docs/reference/plotGenderMarkers-1.png
docs/reference/plotGenderMarkers-2.png
docs/reference/plotGenderMarkers-3.png
docs/reference/plotGenderMarkers.html
docs/reference/plotGene-1.png
docs/reference/plotGene-2.png
docs/reference/plotGene-3.png
docs/reference/plotGene.html
docs/reference/plotGeneSaturation-1.png
docs/reference/plotGeneSaturation-2.png
docs/reference/plotGeneSaturation-3.png
docs/reference/plotGeneSaturation.html
docs/reference/plotGenesDetected-1.png
docs/reference/plotGenesDetected-2.png
docs/reference/plotGenesDetected-3.png
docs/reference/plotGenesDetected-4.png
docs/reference/plotGenesDetected.html
docs/reference/plotHeatmap-1.png
docs/reference/plotHeatmap-2.png
docs/reference/plotHeatmap-3.png
docs/reference/plotHeatmap-4.png
docs/reference/plotHeatmap-5.png
docs/reference/plotHeatmap.html
docs/reference/plotIntronicMappingRate-1.png
docs/reference/plotIntronicMappingRate-2.png
docs/reference/plotIntronicMappingRate-3.png
docs/reference/plotIntronicMappingRate.html
docs/reference/plotMA-1.png
docs/reference/plotMA-2.png
docs/reference/plotMA-3.png
docs/reference/plotMA-4.png
docs/reference/plotMA.html
docs/reference/plotMappedReads-1.png
docs/reference/plotMappedReads-2.png
docs/reference/plotMappedReads-3.png
docs/reference/plotMappedReads.html
docs/reference/plotMappingRate-1.png
docs/reference/plotMappingRate-2.png
docs/reference/plotMappingRate-3.png
docs/reference/plotMappingRate.html
docs/reference/plotMeanSD-1.png
docs/reference/plotMeanSD-2.png
docs/reference/plotMeanSD-3.png
docs/reference/plotMeanSD.html
docs/reference/plotPCA-1.png
docs/reference/plotPCA-2.png
docs/reference/plotPCA-3.png
docs/reference/plotPCA-4.png
docs/reference/plotPCA.html
docs/reference/plotPCACovariates-1.png
docs/reference/plotPCACovariates.html
docs/reference/plotRRNAMappingRate-1.png
docs/reference/plotRRNAMappingRate-2.png
docs/reference/plotRRNAMappingRate-3.png
docs/reference/plotRRNAMappingRate.html
docs/reference/plotTotalReads-1.png
docs/reference/plotTotalReads-2.png
docs/reference/plotTotalReads-3.png
docs/reference/plotTotalReads.html
docs/reference/plotVolcano-1.png
docs/reference/plotVolcano-2.png
docs/reference/plotVolcano-3.png
docs/reference/plotVolcano-4.png
docs/reference/plotVolcano.html
docs/reference/prepareRNASeqTemplate.html
docs/reference/reexports.html
docs/reference/resultsTables.html
docs/reference/sampleMetadata.html
docs/reference/subset.html
docs/reference/tmm.html
docs/reference/topTables.html
docs/reference/tpm.html
inst/CITATION
inst/R_scripts/loadRNASeq.R
inst/extdata/bcb.rda
inst/extdata/bcbio/2017-05-23_rnaseq/annotated_combined.counts
inst/extdata/bcbio/2017-05-23_rnaseq/combined.counts
inst/extdata/bcbio/2017-05-23_rnaseq/data_versions.csv
inst/extdata/bcbio/2017-05-23_rnaseq/programs.txt
inst/extdata/bcbio/2017-05-23_rnaseq/project-summary.yaml
inst/extdata/bcbio/2017-05-23_rnaseq/tx2gene.csv
inst/extdata/bcbio/LICENSE
inst/extdata/bcbio/README.md
inst/extdata/bcbio/group1_1/group1_1-ready.counts
inst/extdata/bcbio/group1_1/salmon/quant.sf
inst/extdata/bcbio/group1_2/group1_2-ready.counts
inst/extdata/bcbio/group1_2/salmon/quant.sf
inst/extdata/bcbio/group2_1/group2_1-ready.counts
inst/extdata/bcbio/group2_1/salmon/quant.sf
inst/extdata/bcbio/group2_2/group2_2-ready.counts
inst/extdata/bcbio/group2_2/salmon/quant.sf
inst/extdata/dds.rda
inst/extdata/res.rda
inst/extdata/rld.rda
inst/extdata/sample_metadata.csv
inst/rmarkdown/shared/_footer.Rmd inst/rmarkdown/shared/_header.Rmd
inst/rmarkdown/shared/_output.yaml
inst/rmarkdown/shared/bibliography.bib
inst/rmarkdown/shared/setup.R inst/rmarkdown/templates/differential_expression/skeleton/skeleton.Rmd
inst/rmarkdown/templates/differential_expression/template.yaml
inst/rmarkdown/templates/functional_analysis/skeleton/skeleton.Rmd
inst/rmarkdown/templates/functional_analysis/template.yaml
inst/rmarkdown/templates/quality_control/skeleton/skeleton.Rmd
inst/rmarkdown/templates/quality_control/template.yaml
man/AllGenerics.Rd man/aggregateReplicates.Rd man/alphaSummary.Rd man/annotable.Rd man/bcbio.Rd man/bcbioRNADataSet-class.Rd man/bcbioRNASeq-class.Rd man/bcbioRNASeq-package.Rd man/coerce.Rd man/colData.Rd man/counts.Rd man/deprecated.Rd man/design.Rd man/flatFiles.Rd man/genderMarkers.Rd man/gene2symbol.Rd man/interestingGroups.Rd man/loadRNASeq.Rd man/meltLog10.Rd man/metrics.Rd man/plot53Bias.Rd man/plotCorrelationHeatmap.Rd man/plotCountDensity.Rd man/plotCountsPerGene.Rd man/plotDEGHeatmap.Rd man/plotDispEsts.Rd man/plotExonicMappingRate.Rd man/plotGenderMarkers.Rd man/plotGene.Rd man/plotGeneSaturation.Rd man/plotGenesDetected.Rd man/plotHeatmap.Rd man/plotIntronicMappingRate.Rd man/plotMA.Rd man/plotMappedReads.Rd man/plotMappingRate.Rd man/plotMeanSD.Rd man/plotPCA.Rd man/plotPCACovariates.Rd man/plotRRNAMappingRate.Rd man/plotTotalReads.Rd man/plotVolcano.Rd man/prepareRNASeqTemplate.Rd man/reexports.Rd man/resultsTables.Rd man/sampleMetadata.Rd man/subset.Rd man/tmm.Rd man/topTables.Rd man/tpm.Rd
pkgdown/extra.css
tests/testthat.R tests/testthat/test_alphaSummary.R tests/testthat/test_annotable.R tests/testthat/test_deprecated.R tests/testthat/test_flatFiles.R tests/testthat/test_interestingGroups.R tests/testthat/test_internal.R tests/testthat/test_loadRNASeq.R tests/testthat/test_plot53Bias.R tests/testthat/test_plotCorrelationHeatmap.R tests/testthat/test_plotCountDensity.R tests/testthat/test_plotCountsPerGene.R tests/testthat/test_plotDEGHeatmap.R tests/testthat/test_plotDispEsts.R tests/testthat/test_plotExonicMappingRate.R tests/testthat/test_plotGenderMarkers.R tests/testthat/test_plotGene.R tests/testthat/test_plotGeneSaturation.R tests/testthat/test_plotGenesDetected.R tests/testthat/test_plotHeatmap.R tests/testthat/test_plotIntronicMappingRate.R tests/testthat/test_plotMA.R tests/testthat/test_plotMappedReads.R tests/testthat/test_plotMappingRate.R tests/testthat/test_plotMeanSD.R tests/testthat/test_plotPCA.R tests/testthat/test_plotPCACovariates.R tests/testthat/test_plotRRNAMappingRate.R tests/testthat/test_plotTotalReads.R tests/testthat/test_plotVolcano.R tests/testthat/test_prepareRNASeqTemplate.R tests/testthat/test_resultsTables.R tests/testthat/test_subset.R tests/testthat/test_topTables.R
hbc/bcbioRNASeq documentation built on Dec. 13, 2017, 2:10 p.m.