Files in bedapub/ribiosNGS
Utilities for next-generation sequencing data analysis in ribios

.Rbuildignore

.github/.gitignore

.github/workflows/standard-ci-workflow.yml

.gitignore

DESCRIPTION

Makefile

NAMESPACE

NEWS

R/20210217-toribios.R R/AllClasses.R R/AllGenerics.R R/AllMethods.R R/DGEListToLongTable.R R/EdgeObject.R R/annotateMethods.R R/appendZScore.R R/dge.R R/dgeTable.R R/edgeR-funcs.R R/edgeR-slurm-lsf.R R/eset2DGEList.R R/exportEdgeResult.R R/filterByCPM.R R/knockdown.R R/logFCmatrix.R R/logFCpca.R R/mergeDGEList.R R/minGroupCount.R R/mps-io.R R/normalize.R R/pca.R R/plotMethods.R R/plotTopSigGenes.R R/pseudoT.R R/readBiokitAsDGEList.R R/readFeatureAnnotationForEdgeR.R R/readSampleAnnotationForEdgeR.R R/renameContrast.R R/ribiosNGS-package.R R/split.DGEList.R R/staticGeneLevelPlots.R R/sva.R R/svaseqRemove.R R/topDgeExpression.R R/tpm.R R/utils.R R/voomLimma.R R/writeBiokitSampleAnnotation.R R/writeDGEList.R README.md

inst/Rscripts/merge.Rscript

inst/extdata/AmpliSeq_files/BarcodeSummaryFile-1.xls

inst/extdata/AmpliSeq_files/BarcodeSummaryFile-2.xls

inst/extdata/AmpliSeq_files/BarcodeSummaryFile-3.xls

inst/extdata/AmpliSeq_files/MolPhen-coverage-example-20200115.gct

inst/extdata/AmpliSeq_files/PathwayReporterGenesV4-Immune-Tox-Lyso-20190905.bed

inst/extdata/AmpliSeq_files/ReadCountFile-1.xls

inst/extdata/AmpliSeq_files/ReadCountFile-2.xls

inst/extdata/AmpliSeq_files/ReadCountFile-3.xls

inst/extdata/biokit_expression_files/biokit-output-1.expression

inst/extdata/biokit_expression_files/biokit-output-2.expression

inst/extdata/biokit_expression_files/biokit-output-3.expression

inst/extdata/biokit_expression_files/biokit-output-4.expression

inst/extdata/mpsnake-minimal-outdir/results/annot/feature.annot

inst/extdata/mpsnake-minimal-outdir/results/annot/phenoData.meta

inst/extdata/mpsnake-minimal-outdir/results/annot/unnamed-molphen-project.gct

inst/extdata/mpsnake-minimal-outdir/results/gct/unnamed-molphen-project.gct

inst/extdata/phenoData/test-phenoData.txt

inst/extdata/sage/Targets25.txt

inst/extdata/sage/sample1.txt

inst/extdata/sage/sample2.txt

inst/extdata/sage/sample3.txt

inst/extdata/sage/sample4.txt

inst/rmarkdown/templates/edgeR-report/skeleton/skeleton.Rmd

inst/rmarkdown/templates/edgeR-report/template.yaml

ribiosNGS.Rproj

tests/testthat.R tests/testthat/test-appendZScore.R tests/testthat/test-checkBiokitSampleAnnotation.R tests/testthat/test-classes.R tests/testthat/test-dgeWithLimmaVoom.R tests/testthat/test-edgeRcommand.R tests/testthat/test-pseudoTfromPvalue.R tests/testthat/test-readMolPhenCoverageGct.R tests/testthat/test-readMpsnakeAsDGEList.R

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.

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bedapub/ribiosNGS
Utilities for next-generation sequencing data analysis in ribios

Files in bedapub/ribiosNGS
Utilities for next-generation sequencing data analysis in ribios

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bedapub/ribiosNGS Utilities for next-generation sequencing data analysis in ribios

Files in bedapub/ribiosNGS Utilities for next-generation sequencing data analysis in ribios

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We want your feedback!

bedapub/ribiosNGS
Utilities for next-generation sequencing data analysis in ribios

Files in bedapub/ribiosNGS
Utilities for next-generation sequencing data analysis in ribios