Files in hbc/bcbioRnaseq
RNA-Seq Utilities

.Rbuildignore
.gitignore
.lintr
.travis.yml
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS
NEWS.md R/AllClasses.R R/AllGenerics.R R/DESeqDataSet-internal.R R/aggregateReplicates-methods.R R/alphaSummary-methods.R R/bcbioRNASeq-constructor.R R/bcbioRNASeq-package.R R/bcbioRNASeq-validity.R R/coerce-methods.R R/contrastName-methods.R R/counts-methods.R R/data.R R/deprecated.R R/extract-methods.R R/general.R R/ggplot2-internal.R R/globals.R R/melt-internal.R R/metrics-methods.R R/new-internal.R R/nonzeroGenes-internal.R R/plot5Prime3PrimeBias-methods.R R/plotCorrelationHeatmap-methods.R R/plotCountDensity-methods.R R/plotCountsPerGene-methods.R R/plotDEGHeatmap-methods.R R/plotDEGPCA-methods.R R/plotDispEsts-methods.R R/plotExonicMappingRate-methods.R R/plotGenderMarkers-methods.R R/plotGene-methods.R R/plotGeneSaturation-methods.R R/plotGenesDetected-methods.R R/plotIntronicMappingRate-methods.R R/plotMA-methods.R R/plotMappedReads-methods.R R/plotMappingRate-methods.R R/plotMeanSD-methods.R R/plotPCA-methods.R R/plotPCACovariates-methods.R R/plotRRNAMappingRate-methods.R R/plotTotalReads-methods.R R/plotVolcano-methods.R R/prepareRNASeqTemplate-methods.R R/resultsTables-methods.R R/sampleData-methods.R R/show-methods.R R/tmm-methods.R R/topTables-methods.R R/tpm-methods.R R/tximport-internal.R R/updateObject-methods.R README.md
_pkgdown.yml
appveyor.yml
bcbioRNASeq.Rproj
data-raw/.gitignore
data-raw/01_gender_markers.R data-raw/02_bcb_small.R data-raw/03_dds_small.R
data-raw/gender_markers.xlsx
data/bcb_small.rda
data/dds_small.rda
data/gender_markers.rda
data/res_small.rda
docs/CONTRIBUTING.html
docs/LICENSE-text.html
docs/articles/bcbioRNASeq.html
docs/articles/index.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/extra.css
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/aggregateReplicates.html
docs/reference/alphaSummary.html
docs/reference/bcb_small.html
docs/reference/bcbioRNASeq-package.html
docs/reference/bcbioRNASeq.html
docs/reference/coerce.html
docs/reference/contrastName.html
docs/reference/counts.html
docs/reference/dds_small.html
docs/reference/deprecated.html
docs/reference/extract.html
docs/reference/gender_markers.html
docs/reference/general.html
docs/reference/index.html
docs/reference/metrics.html
docs/reference/plot5Prime3PrimeBias-1.png
docs/reference/plot5Prime3PrimeBias.html
docs/reference/plotCorrelationHeatmap-1.png
docs/reference/plotCorrelationHeatmap-2.png
docs/reference/plotCorrelationHeatmap.html
docs/reference/plotCountDensity-1.png
docs/reference/plotCountDensity.html
docs/reference/plotCountsPerGene-1.png
docs/reference/plotCountsPerGene.html
docs/reference/plotDEGHeatmap-1.png
docs/reference/plotDEGHeatmap-2.png
docs/reference/plotDEGHeatmap-3.png
docs/reference/plotDEGHeatmap.html
docs/reference/plotDEGPCA-1.png
docs/reference/plotDEGPCA-2.png
docs/reference/plotDEGPCA.html
docs/reference/plotDispEsts-1.png
docs/reference/plotDispEsts-2.png
docs/reference/plotDispEsts.html
docs/reference/plotExonicMappingRate-1.png
docs/reference/plotExonicMappingRate.html
docs/reference/plotGenderMarkers-1.png
docs/reference/plotGenderMarkers-2.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.html
docs/reference/plotGenesDetected-1.png
docs/reference/plotGenesDetected.html
docs/reference/plotIntronicMappingRate-1.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-5.png
docs/reference/plotMA.html
docs/reference/plotMappedReads-1.png
docs/reference/plotMappedReads.html
docs/reference/plotMappingRate-1.png
docs/reference/plotMappingRate.html
docs/reference/plotMeanSD-1.png
docs/reference/plotMeanSD-2.png
docs/reference/plotMeanSD.html
docs/reference/plotPCA-1.png
docs/reference/plotPCA-2.png
docs/reference/plotPCA.html
docs/reference/plotPCACovariates-1.png
docs/reference/plotPCACovariates.html
docs/reference/plotRRNAMappingRate-1.png
docs/reference/plotRRNAMappingRate.html
docs/reference/plotTotalReads-1.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/res_small.html
docs/reference/resultsTables.html
docs/reference/sampleData.html
docs/reference/show.html
docs/reference/tmm.html
docs/reference/topTables.html
docs/reference/tpm.html
docs/reference/updateObject.html
inst/CITATION
inst/extdata/bcbio/2017-05-23_rnaseq/bcbio-nextgen-commands.log
inst/extdata/bcbio/2017-05-23_rnaseq/bcbio-nextgen.log
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/group1_1/salmon/quant.sf
inst/extdata/bcbio/group1_2/salmon/quant.sf
inst/extdata/bcbio/group2_1/salmon/quant.sf
inst/extdata/bcbio/group2_2/salmon/quant.sf
inst/extdata/bcbio/sample_metadata.csv
inst/rmarkdown/shared/_footer.Rmd inst/rmarkdown/shared/_header.Rmd
inst/rmarkdown/shared/_output.yaml
inst/rmarkdown/shared/_setup.R
inst/rmarkdown/shared/bibliography.bib
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/aggregateReplicates.Rd man/alphaSummary.Rd man/bcb_small.Rd man/bcbioRNASeq-package.Rd man/bcbioRNASeq.Rd man/coerce.Rd man/contrastName.Rd man/counts.Rd man/dds_small.Rd man/deprecated.Rd man/extract.Rd man/gender_markers.Rd man/general.Rd man/metrics.Rd man/plot5Prime3PrimeBias.Rd man/plotCorrelationHeatmap.Rd man/plotCountDensity.Rd man/plotCountsPerGene.Rd man/plotDEGHeatmap.Rd man/plotDEGPCA.Rd man/plotDispEsts.Rd man/plotExonicMappingRate.Rd man/plotGenderMarkers.Rd man/plotGene.Rd man/plotGeneSaturation.Rd man/plotGenesDetected.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/res_small.Rd man/resultsTables.Rd man/sampleData.Rd man/show.Rd man/tmm.Rd man/topTables.Rd man/tpm.Rd man/updateObject.Rd
pkgdown/extra.css
tests/testthat.R
tests/testthat/.gitignore
tests/testthat/helper_01_cache.R tests/testthat/helper_02_globals.R tests/testthat/test_data_functions.R tests/testthat/test_differential_expression_functions.R tests/testthat/test_gene_expression_functions.R tests/testthat/test_quality_control_functions.R tests/testthat/test_rmarkdown_functions.R tests/testthat/test_s4_object.R
travis_render.sh
vignettes/.gitignore
vignettes/bcbioRNASeq.Rmd
hbc/bcbioRnaseq documentation built on Nov. 3, 2018, 2:23 p.m.