Files in gofflab/cummeRbund-BioC-Bridge
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
.Rapp.history
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/AllClasses.R
R/AllGenerics.R
R/database-setup.R
R/methods-CuffData.R
R/methods-CuffDist.R
R/methods-CuffFeature.R
R/methods-CuffFeatureSet.R
R/methods-CuffGene.R
R/methods-CuffGeneSet.R
R/methods-CuffSet.R
R/tools.R
README
data/sampleData.RData
data/sampleData.rda
inst/NEWS
inst/extdata/cds.count_tracking
inst/extdata/cds.diff
inst/extdata/cds.fpkm_tracking
inst/extdata/cds.read_group_tracking
inst/extdata/cds_exp.diff
inst/extdata/chr1_snippet.gtf
inst/extdata/cuffData_schema.sql
inst/extdata/gene_exp.diff
inst/extdata/genes.count_tracking
inst/extdata/genes.fpkm_tracking
inst/extdata/genes.read_group_tracking
inst/extdata/isoform_exp.diff
inst/extdata/isoforms.count_tracking
inst/extdata/isoforms.fpkm_tracking
inst/extdata/isoforms.read_group_tracking
inst/extdata/promoters.diff
inst/extdata/read_groups.info
inst/extdata/run.info
inst/extdata/splicing.diff
inst/extdata/tss_group_exp.diff
inst/extdata/tss_groups.count_tracking
inst/extdata/tss_groups.fpkm_tracking
inst/extdata/tss_groups.read_group_tracking
inst/reports/runReport.Rmd
inst/reports/styles/report_style.css
man/CuffData-class.Rd
man/CuffDist-class.Rd
man/CuffFeature-class.Rd
man/CuffFeatureSet-class.Rd
man/CuffGene-class.Rd
man/CuffGeneSet-class.Rd
man/CuffSet-class.Rd
man/JSdist.Rd
man/JSdistFromP.Rd
man/JSdistVec.Rd
man/MAplot.Rd
man/PINK1.Rd
man/QCplots.Rd
man/addFeatures.Rd
man/count.Rd
man/countMatrix.Rd
man/csBoxplot.Rd
man/csCluster.Rd
man/csClusterPlot.Rd
man/csDendro.Rd
man/csDensity.Rd
man/csDistHeat.Rd
man/csHeatmap.Rd
man/csScatter.Rd
man/csSpecificity.Rd
man/csVolcano.Rd
man/cummeRbund-package.Rd
man/diffData.Rd
man/dimensionality.Rd
man/dispersionPlot.Rd
man/distValues.Rd
man/exploratory.Rd
man/expressionBarplot.Rd
man/expressionPlot.Rd
man/featureNames.Rd
man/features.Rd
man/findGene.Rd
man/findSimilar.Rd
man/fpkm.Rd
man/fpkmMatrix.Rd
man/getFeatures.Rd
man/getGene.Rd
man/getGeneId.Rd
man/getGenes.Rd
man/getLevels.Rd
man/getRepLevels.Rd
man/getSig.Rd
man/getSigTable.Rd
man/makeprobs.Rd
man/makeprobsvec.Rd
man/readCufflinks.Rd
man/repFpkm.Rd
man/replicates.Rd
man/runInfo.Rd
man/sampleGeneSet.Rd
man/sampleIDs.Rd
man/samples.Rd
man/shannon.entropy.Rd
man/sigMatrix.Rd
vignettes/ENCODE_SCV.pdf
vignettes/cuffData_schema.pdf
vignettes/cummeRbund-example-workflow.Rnw
vignettes/cummeRbund-manual.Rnw
