Files in alyssafrazee/ballgown
Flexible, isoform-level differential expression analysis
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/AllClass.R
R/AllGenerics.R
R/annotate_assembly.R
R/assessSim.R
R/ballgown-expr-methods.R
R/ballgown-get-methods.R
R/ballgown-package.R
R/ballgown-replace-methods.R
R/ballgown-show-method.R
R/ballgown-subset-method.R
R/ballgownrsem.R
R/bg-data.R
R/checkAssembledTx.R
R/closestColor.R
R/clusterTranscripts.R
R/collapseTranscripts.R
R/constructor.R
R/contains.R
R/exprfilter.R
R/getAttributeField.R
R/getGenes.R
R/gffRead.R
R/gffReadGR.R
R/last.R
R/pctOverlap.R
R/plotLatentTranscripts.R
R/plotMeans.R
R/plotTranscripts.R
R/ss.R
R/stattest.R
R/tGene.R
R/writeFiles.R
README.html
README.md
data/bg.rda
figure/clusterviz-1.png
figure/clusterviz.png
figure/plotMeans-1.png
figure/plotMeans.png
figure/plotTranscript.png
figure/plotTranscripts-1.png
figure/plotTranscripts.png
figure/plotTranscripts2-1.png
figure/plotTranscripts2.png
inst/extdata/annot.gtf.gz
inst/extdata/hg19_genes_small.gtf.gz
inst/extdata/sample01/e2t.ctab
inst/extdata/sample01/e_data.ctab
inst/extdata/sample01/i2t.ctab
inst/extdata/sample01/i_data.ctab
inst/extdata/sample01/t_data.ctab
inst/extdata/sample02/e2t.ctab
inst/extdata/sample02/e_data.ctab
inst/extdata/sample02/i2t.ctab
inst/extdata/sample02/i_data.ctab
inst/extdata/sample02/t_data.ctab
inst/extdata/sample03/e2t.ctab
inst/extdata/sample03/e_data.ctab
inst/extdata/sample03/i2t.ctab
inst/extdata/sample03/i_data.ctab
inst/extdata/sample03/t_data.ctab
inst/extdata/sample04/e2t.ctab
inst/extdata/sample04/e_data.ctab
inst/extdata/sample04/i2t.ctab
inst/extdata/sample04/i_data.ctab
inst/extdata/sample04/t_data.ctab
inst/extdata/sample05/e2t.ctab
inst/extdata/sample05/e_data.ctab
inst/extdata/sample05/i2t.ctab
inst/extdata/sample05/i_data.ctab
inst/extdata/sample05/t_data.ctab
inst/extdata/sample06/e2t.ctab
inst/extdata/sample06/e_data.ctab
inst/extdata/sample06/i2t.ctab
inst/extdata/sample06/i_data.ctab
inst/extdata/sample06/t_data.ctab
inst/extdata/sample07/e2t.ctab
inst/extdata/sample07/e_data.ctab
inst/extdata/sample07/i2t.ctab
inst/extdata/sample07/i_data.ctab
inst/extdata/sample07/t_data.ctab
inst/extdata/sample08/e2t.ctab
inst/extdata/sample08/e_data.ctab
inst/extdata/sample08/i2t.ctab
inst/extdata/sample08/i_data.ctab
inst/extdata/sample08/t_data.ctab
inst/extdata/sample09/e2t.ctab
inst/extdata/sample09/e_data.ctab
inst/extdata/sample09/i2t.ctab
inst/extdata/sample09/i_data.ctab
inst/extdata/sample09/t_data.ctab
inst/extdata/sample10/e2t.ctab
inst/extdata/sample10/e_data.ctab
inst/extdata/sample10/i2t.ctab
inst/extdata/sample10/i_data.ctab
inst/extdata/sample10/t_data.ctab
inst/extdata/sample11/e2t.ctab
inst/extdata/sample11/e_data.ctab
inst/extdata/sample11/i2t.ctab
inst/extdata/sample11/i_data.ctab
inst/extdata/sample11/t_data.ctab
inst/extdata/sample12/e2t.ctab
inst/extdata/sample12/e_data.ctab
inst/extdata/sample12/i2t.ctab
inst/extdata/sample12/i_data.ctab
inst/extdata/sample12/t_data.ctab
inst/extdata/sample13/e2t.ctab
inst/extdata/sample13/e_data.ctab
inst/extdata/sample13/i2t.ctab
inst/extdata/sample13/i_data.ctab
inst/extdata/sample13/t_data.ctab
inst/extdata/sample14/e2t.ctab
inst/extdata/sample14/e_data.ctab
inst/extdata/sample14/i2t.ctab
inst/extdata/sample14/i_data.ctab
inst/extdata/sample14/t_data.ctab
inst/extdata/sample15/e2t.ctab
inst/extdata/sample15/e_data.ctab
inst/extdata/sample15/i2t.ctab
inst/extdata/sample15/i_data.ctab
inst/extdata/sample15/t_data.ctab
inst/extdata/sample16/e2t.ctab
inst/extdata/sample16/e_data.ctab
inst/extdata/sample16/i2t.ctab
inst/extdata/sample16/i_data.ctab
inst/extdata/sample16/t_data.ctab
inst/extdata/sample17/e2t.ctab
inst/extdata/sample17/e_data.ctab
inst/extdata/sample17/i2t.ctab
inst/extdata/sample17/i_data.ctab
inst/extdata/sample17/t_data.ctab
inst/extdata/sample18/e2t.ctab
inst/extdata/sample18/e_data.ctab
inst/extdata/sample18/i2t.ctab
inst/extdata/sample18/i_data.ctab
inst/extdata/sample18/t_data.ctab
inst/extdata/sample19/e2t.ctab
inst/extdata/sample19/e_data.ctab
inst/extdata/sample19/i2t.ctab
inst/extdata/sample19/i_data.ctab
inst/extdata/sample19/t_data.ctab
inst/extdata/sample20/e2t.ctab
inst/extdata/sample20/e_data.ctab
inst/extdata/sample20/i2t.ctab
inst/extdata/sample20/i_data.ctab
inst/extdata/sample20/t_data.ctab
inst/extdata/tiny.genes.results.gz
inst/extdata/tiny.isoforms.results.gz
inst/extdata/tiny2.genes.results.gz
inst/extdata/tiny2.isoforms.results.gz
man/annotate_assembly.Rd
man/ballgown-class.Rd
man/ballgown-constructor.Rd
man/ballgown-package.Rd
man/ballgownrsem.Rd
man/bg.Rd
man/checkAssembledTx.Rd
man/clusterTranscripts.Rd
man/collapseTranscripts.Rd
man/contains.Rd
man/dirs.Rd
man/eexpr.Rd
man/expr-replace.Rd
man/expr.Rd
man/exprfilter.Rd
man/geneIDs.Rd
man/geneNames.Rd
man/getAttributeField.Rd
man/getGenes.Rd
man/gexpr.Rd
man/gffRead.Rd
man/gffReadGR.Rd
man/iexpr.Rd
man/indexes-replace.Rd
man/indexes.Rd
man/last.Rd
man/mergedDate.Rd
man/pData-replace.Rd
man/pData.Rd
man/pctOverlap.Rd
man/plotLatentTranscripts.Rd
man/plotMeans.Rd
man/plotTranscripts.Rd
man/sampleNames.Rd
man/seqnames.Rd
man/stattest.Rd
man/structure.Rd
man/subset.Rd
man/tGene.Rd
man/texpr.Rd
man/transcriptIDs.Rd
man/transcriptNames.Rd
man/writeFiles.Rd
tests/test-all.R
tests/testthat/test-annotation.R
tests/testthat/test-constructor.R
tests/testthat/test-plots.R
tests/testthat/test-stats.R
vignettes/ballgown.Rmd
vignettes/ballgown.html
