ballgown: Flexible, isoform-level differential expression analysis

Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.

AuthorJack Fu [aut], Alyssa C. Frazee [aut, cre], Leonardo Collado-Torres [aut], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Date of publicationNone
MaintainerJack Fu <jmfu@jhsph.edu>
LicenseArtistic-2.0
Version2.6.0

View on Bioconductor

Man pages

annotate_assembly: match assembled transcripts to annotated transcripts

ballgown-class: Ballgown

ballgown-constructor: constructor function for ballgown objects

ballgown-package: The ballgown package for analysis of transcript assemblies

ballgownrsem: load RSEM data into a ballgown object

bg: Toy ballgown object

checkAssembledTx: plot annotated and assembled transcripts together

clusterTranscripts: group a gene's assembled transcripts into clusters

collapseTranscripts: cluster a gene's transcripts and calculate cluster-level...

contains: determine if one set of GRanges fully contains any of another...

dirs: extract paths to tablemaker output

eexpr: extract exon-level expression measurements from ballgown...

expr: extract expression components from ballgown objects

exprfilter: subset ballgown objects using an expression filter

expr-replace: Replacement method for expr slot in ballgown objects

geneIDs: get gene IDs from a ballgown object

geneNames: get gene names from a ballgown object

getAttributeField: extract a specific field of the "attributes" column of a data...

getGenes: label assembled transcripts with gene names

gexpr: extract gene-level expression measurements from ballgown...

gffRead: read in GTF/GFF file as a data frame

gffReadGR: read in gtf file as GRanges object

iexpr: extract transcript-level expression measurements from...

indexes: extract the indexes from ballgown objects

indexes-replace: Replace method for indexes slot in ballgown objects

last: get the last element

mergedDate: extract package version & creation date from ballgown object

pctOverlap: calculate percent overlap between two GRanges objects

pData: extract phenotype data from a ballgown object

pData-replace: Replacement method for pData slot in ballgown objects

plotLatentTranscripts: cluster assembled transcripts and plot the results

plotMeans: visualize transcript abundance by group

plotTranscripts: visualize structure of assembled transcripts

sampleNames: get names of samples in a ballgown objects

seqnames: get sequence (chromosome) names from ballgown object

stattest: statistical tests for differential expression in ballgown

structure: extract structure components from ballgown objects

subset: subset ballgown objects to specific samples or genomic...

texpr: extract transcript-level expression measurements from...

tGene: Connect a transcript to its gene

transcriptIDs: get numeric transcript IDs from a ballgown object

transcriptNames: get transcript names from a ballgown object

writeFiles: write files to disk from ballgown object

Files in this package

ballgown/DESCRIPTION
ballgown/NAMESPACE
ballgown/NEWS
ballgown/R
ballgown/R/AllClass.R ballgown/R/AllGenerics.R ballgown/R/annotate_assembly.R ballgown/R/assessSim.R ballgown/R/ballgown-expr-methods.R ballgown/R/ballgown-get-methods.R ballgown/R/ballgown-package.R ballgown/R/ballgown-replace-methods.R ballgown/R/ballgown-show-method.R ballgown/R/ballgown-subset-method.R ballgown/R/ballgownrsem.R ballgown/R/bg-data.R ballgown/R/checkAssembledTx.R ballgown/R/closestColor.R ballgown/R/clusterTranscripts.R ballgown/R/collapseTranscripts.R ballgown/R/constructor.R ballgown/R/contains.R ballgown/R/exprfilter.R ballgown/R/getAttributeField.R ballgown/R/getGenes.R ballgown/R/gffRead.R ballgown/R/gffReadGR.R ballgown/R/last.R ballgown/R/pctOverlap.R ballgown/R/plotLatentTranscripts.R ballgown/R/plotMeans.R ballgown/R/plotTranscripts.R ballgown/R/ss.R ballgown/R/stattest.R ballgown/R/tGene.R ballgown/R/writeFiles.R
ballgown/README.html
ballgown/build
ballgown/build/vignette.rds
ballgown/data
ballgown/data/bg.rda
ballgown/inst
ballgown/inst/doc
ballgown/inst/doc/ballgown.R
ballgown/inst/doc/ballgown.Rmd
ballgown/inst/doc/ballgown.html
ballgown/inst/extdata
ballgown/inst/extdata/annot.gtf.gz
ballgown/inst/extdata/hg19_genes_small.gtf.gz
ballgown/inst/extdata/sample01
ballgown/inst/extdata/sample01/e2t.ctab
ballgown/inst/extdata/sample01/e_data.ctab
ballgown/inst/extdata/sample01/i2t.ctab
ballgown/inst/extdata/sample01/i_data.ctab
ballgown/inst/extdata/sample01/t_data.ctab
ballgown/inst/extdata/sample02
ballgown/inst/extdata/sample02/e2t.ctab
ballgown/inst/extdata/sample02/e_data.ctab
ballgown/inst/extdata/sample02/i2t.ctab
ballgown/inst/extdata/sample02/i_data.ctab
ballgown/inst/extdata/sample02/t_data.ctab
ballgown/inst/extdata/sample03
ballgown/inst/extdata/sample03/e2t.ctab
ballgown/inst/extdata/sample03/e_data.ctab
ballgown/inst/extdata/sample03/i2t.ctab
ballgown/inst/extdata/sample03/i_data.ctab
ballgown/inst/extdata/sample03/t_data.ctab
ballgown/inst/extdata/sample04
ballgown/inst/extdata/sample04/e2t.ctab
ballgown/inst/extdata/sample04/e_data.ctab
ballgown/inst/extdata/sample04/i2t.ctab
ballgown/inst/extdata/sample04/i_data.ctab
ballgown/inst/extdata/sample04/t_data.ctab
ballgown/inst/extdata/sample05
ballgown/inst/extdata/sample05/e2t.ctab
ballgown/inst/extdata/sample05/e_data.ctab
ballgown/inst/extdata/sample05/i2t.ctab
ballgown/inst/extdata/sample05/i_data.ctab
ballgown/inst/extdata/sample05/t_data.ctab
ballgown/inst/extdata/sample06
ballgown/inst/extdata/sample06/e2t.ctab
ballgown/inst/extdata/sample06/e_data.ctab
ballgown/inst/extdata/sample06/i2t.ctab
ballgown/inst/extdata/sample06/i_data.ctab
ballgown/inst/extdata/sample06/t_data.ctab
ballgown/inst/extdata/sample07
ballgown/inst/extdata/sample07/e2t.ctab
ballgown/inst/extdata/sample07/e_data.ctab
ballgown/inst/extdata/sample07/i2t.ctab
ballgown/inst/extdata/sample07/i_data.ctab
ballgown/inst/extdata/sample07/t_data.ctab
ballgown/inst/extdata/sample08
ballgown/inst/extdata/sample08/e2t.ctab
ballgown/inst/extdata/sample08/e_data.ctab
ballgown/inst/extdata/sample08/i2t.ctab
ballgown/inst/extdata/sample08/i_data.ctab
ballgown/inst/extdata/sample08/t_data.ctab
ballgown/inst/extdata/sample09
ballgown/inst/extdata/sample09/e2t.ctab
ballgown/inst/extdata/sample09/e_data.ctab
ballgown/inst/extdata/sample09/i2t.ctab
ballgown/inst/extdata/sample09/i_data.ctab
ballgown/inst/extdata/sample09/t_data.ctab
ballgown/inst/extdata/sample10
ballgown/inst/extdata/sample10/e2t.ctab
ballgown/inst/extdata/sample10/e_data.ctab
ballgown/inst/extdata/sample10/i2t.ctab
ballgown/inst/extdata/sample10/i_data.ctab
ballgown/inst/extdata/sample10/t_data.ctab
ballgown/inst/extdata/sample11
ballgown/inst/extdata/sample11/e2t.ctab
ballgown/inst/extdata/sample11/e_data.ctab
ballgown/inst/extdata/sample11/i2t.ctab
ballgown/inst/extdata/sample11/i_data.ctab
ballgown/inst/extdata/sample11/t_data.ctab
ballgown/inst/extdata/sample12
ballgown/inst/extdata/sample12/e2t.ctab
ballgown/inst/extdata/sample12/e_data.ctab
ballgown/inst/extdata/sample12/i2t.ctab
ballgown/inst/extdata/sample12/i_data.ctab
ballgown/inst/extdata/sample12/t_data.ctab
ballgown/inst/extdata/sample13
ballgown/inst/extdata/sample13/e2t.ctab
ballgown/inst/extdata/sample13/e_data.ctab
ballgown/inst/extdata/sample13/i2t.ctab
ballgown/inst/extdata/sample13/i_data.ctab
ballgown/inst/extdata/sample13/t_data.ctab
ballgown/inst/extdata/sample14
ballgown/inst/extdata/sample14/e2t.ctab
ballgown/inst/extdata/sample14/e_data.ctab
ballgown/inst/extdata/sample14/i2t.ctab
ballgown/inst/extdata/sample14/i_data.ctab
ballgown/inst/extdata/sample14/t_data.ctab
ballgown/inst/extdata/sample15
ballgown/inst/extdata/sample15/e2t.ctab
ballgown/inst/extdata/sample15/e_data.ctab
ballgown/inst/extdata/sample15/i2t.ctab
ballgown/inst/extdata/sample15/i_data.ctab
ballgown/inst/extdata/sample15/t_data.ctab
ballgown/inst/extdata/sample16
ballgown/inst/extdata/sample16/e2t.ctab
ballgown/inst/extdata/sample16/e_data.ctab
ballgown/inst/extdata/sample16/i2t.ctab
ballgown/inst/extdata/sample16/i_data.ctab
ballgown/inst/extdata/sample16/t_data.ctab
ballgown/inst/extdata/sample17
ballgown/inst/extdata/sample17/e2t.ctab
ballgown/inst/extdata/sample17/e_data.ctab
ballgown/inst/extdata/sample17/i2t.ctab
ballgown/inst/extdata/sample17/i_data.ctab
ballgown/inst/extdata/sample17/t_data.ctab
ballgown/inst/extdata/sample18
ballgown/inst/extdata/sample18/e2t.ctab
ballgown/inst/extdata/sample18/e_data.ctab
ballgown/inst/extdata/sample18/i2t.ctab
ballgown/inst/extdata/sample18/i_data.ctab
ballgown/inst/extdata/sample18/t_data.ctab
ballgown/inst/extdata/sample19
ballgown/inst/extdata/sample19/e2t.ctab
ballgown/inst/extdata/sample19/e_data.ctab
ballgown/inst/extdata/sample19/i2t.ctab
ballgown/inst/extdata/sample19/i_data.ctab
ballgown/inst/extdata/sample19/t_data.ctab
ballgown/inst/extdata/sample20
ballgown/inst/extdata/sample20/e2t.ctab
ballgown/inst/extdata/sample20/e_data.ctab
ballgown/inst/extdata/sample20/i2t.ctab
ballgown/inst/extdata/sample20/i_data.ctab
ballgown/inst/extdata/sample20/t_data.ctab
ballgown/inst/extdata/tiny.genes.results.gz
ballgown/inst/extdata/tiny.isoforms.results.gz
ballgown/inst/extdata/tiny2.genes.results.gz
ballgown/inst/extdata/tiny2.isoforms.results.gz
ballgown/man
ballgown/man/annotate_assembly.Rd ballgown/man/ballgown-class.Rd ballgown/man/ballgown-constructor.Rd ballgown/man/ballgown-package.Rd ballgown/man/ballgownrsem.Rd ballgown/man/bg.Rd ballgown/man/checkAssembledTx.Rd ballgown/man/clusterTranscripts.Rd ballgown/man/collapseTranscripts.Rd ballgown/man/contains.Rd ballgown/man/dirs.Rd ballgown/man/eexpr.Rd ballgown/man/expr-replace.Rd ballgown/man/expr.Rd ballgown/man/exprfilter.Rd ballgown/man/geneIDs.Rd ballgown/man/geneNames.Rd ballgown/man/getAttributeField.Rd ballgown/man/getGenes.Rd ballgown/man/gexpr.Rd ballgown/man/gffRead.Rd ballgown/man/gffReadGR.Rd ballgown/man/iexpr.Rd ballgown/man/indexes-replace.Rd ballgown/man/indexes.Rd ballgown/man/last.Rd ballgown/man/mergedDate.Rd ballgown/man/pData-replace.Rd ballgown/man/pData.Rd ballgown/man/pctOverlap.Rd ballgown/man/plotLatentTranscripts.Rd ballgown/man/plotMeans.Rd ballgown/man/plotTranscripts.Rd ballgown/man/sampleNames.Rd ballgown/man/seqnames.Rd ballgown/man/stattest.Rd ballgown/man/structure.Rd ballgown/man/subset.Rd ballgown/man/tGene.Rd ballgown/man/texpr.Rd ballgown/man/transcriptIDs.Rd ballgown/man/transcriptNames.Rd ballgown/man/writeFiles.Rd
ballgown/tablemaker
ballgown/tablemaker/tablemaker-2.1.1
ballgown/tablemaker/tablemaker-2.1.1/build-aux
ballgown/tablemaker/tablemaker-2.1.1/src
ballgown/tablemaker/tablemaker-2.1.1/src/lemon
ballgown/tablemaker/tablemaker-2.1.1/src/lemon/bits
ballgown/tablemaker/tablemaker-2.1.1/src/lemon/concepts
ballgown/tablemaker/tablemaker-2.1.1/src/locfit
ballgown/tests
ballgown/tests/test-all.R
ballgown/tests/testthat
ballgown/tests/testthat/test-annotation.R
ballgown/tests/testthat/test-constructor.R
ballgown/tests/testthat/test-plots.R
ballgown/tests/testthat/test-stats.R
ballgown/vignettes
ballgown/vignettes/ballgown.Rmd

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