Files in roryk/bcbioRnaseq
RNA-Seq Utilities

.Rbuildignore

.gitignore

.lintr

.push.sh

.travis.yml

CONTRIBUTING.md

DESCRIPTION

LICENSE

NAMESPACE

NEWS

R/AllClasses.R R/AllGenerics.R R/bcbioRNASeq-package.R R/datasets.R R/deprecated.R R/globals.R R/internal-DESeqDataSet.R R/internal-general.R R/internal-ggplot2.R R/internal-melt.R R/internal-new.R R/internal-nonzeroGenes.R R/internal-tximport.R R/methods-alphaSummary.R R/methods-coerce.R R/methods-contrastName.R R/methods-counts.R R/methods-metrics.R R/methods-plot5Prime3PrimeBias.R R/methods-plotCorrelationHeatmap.R R/methods-plotCountDensity.R R/methods-plotCountsPerGene.R R/methods-plotDEGHeatmap.R R/methods-plotDEGPCA.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-plotIntronicMappingRate.R R/methods-plotMappedReads.R R/methods-plotMappingRate.R R/methods-plotMeanAverage.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-show.R R/methods-subset.R R/methods-tmm.R R/methods-topTables.R R/methods-tpm.R R/methods-updateObject.R R/reexports.R README.md

_pkgdown.yml

appveyor.yml

bcbioRNASeq.Rproj

data-raw/01_genderMarkers.R data-raw/02_bcb_small.R data-raw/03_dds_small.R

data-raw/genderMarkers.xlsx

data-raw/testthat-readSampleMetadataFile.R

data/bcb_small.rda

data/dds_small.rda

data/genderMarkers.rda

data/res_small.rda

data/rld_small.rda

docs/CONTRIBUTING.html

docs/LICENSE-text.html

docs/authors.html

docs/docsearch.css

docs/extra.css

docs/index.html

docs/jquery.sticky-kit.min.js

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/alphaSummary.html

docs/reference/bcb_small.html

docs/reference/bcbioRNASeq-class.html

docs/reference/bcbioRNASeq-package.html

docs/reference/coerce.html

docs/reference/contrastName.html

docs/reference/counts.html

docs/reference/dds_small.html

docs/reference/deprecated.html

docs/reference/genderMarkers.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-3.png

docs/reference/plotCorrelationHeatmap-4.png

docs/reference/plotCorrelationHeatmap.html

docs/reference/plotCountDensity-1.png

docs/reference/plotCountDensity-2.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-3.png

docs/reference/plotGenderMarkers.html

docs/reference/plotGene-1.png

docs/reference/plotGene-2.png

docs/reference/plotGene-3.png

docs/reference/plotGene-4.png

docs/reference/plotGene.html

docs/reference/plotGeneSaturation-1.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/plotMappedReads-1.png

docs/reference/plotMappedReads.html

docs/reference/plotMappingRate-1.png

docs/reference/plotMappingRate.html

docs/reference/plotMeanAverage-1.png

docs/reference/plotMeanAverage-2.png

docs/reference/plotMeanAverage-3.png

docs/reference/plotMeanAverage-4.png

docs/reference/plotMeanAverage-5.png

docs/reference/plotMeanAverage.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-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.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/reexports.html

docs/reference/res_small.html

docs/reference/resultsTables.html

docs/reference/rld_small.html

docs/reference/show.html

docs/reference/subset.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/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/alphaSummary.Rd man/bcb_small.Rd man/bcbioRNASeq-class.Rd man/bcbioRNASeq-package.Rd man/coerce.Rd man/contrastName.Rd man/counts.Rd man/dds_small.Rd man/deprecated.Rd man/genderMarkers.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/plotMappedReads.Rd man/plotMappingRate.Rd man/plotMeanAverage.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/res_small.Rd man/resultsTables.Rd man/rld_small.Rd man/show.Rd man/subset.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_class_definition.R

roryk/bcbioRnaseq documentation built on May 27, 2019, 10:44 p.m.

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roryk/bcbioRnaseq
RNA-Seq Utilities

Files in roryk/bcbioRnaseq
RNA-Seq Utilities

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roryk/bcbioRnaseq RNA-Seq Utilities

Files in roryk/bcbioRnaseq RNA-Seq Utilities

R Package Documentation

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roryk/bcbioRnaseq
RNA-Seq Utilities

Files in roryk/bcbioRnaseq
RNA-Seq Utilities