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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ballgown")
AuthorJack Fu [aut], Alyssa C. Frazee [aut, cre], Leonardo Collado-Torres [aut], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Bioconductor views DifferentialExpression Preprocessing RNASeq StatisticalMethod
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

Functions

annotate_assembly Man page
ballgown Man page
Ballgown Man page
ballgown-class Man page
ballgown-constructor Man page
ballgownp Man page
ballgown-package Man page
ballgownrsem Man page
bg Man page
checkAssembledTx Man page
clusterTranscripts Man page
collapseTranscripts Man page
contains Man page
dirs Man page
dirs,ballgown-method Man page
eexpr Man page
eexpr,ballgown-method Man page
expr Man page
expr<- Man page
expr<-,ballgown-method Man page
expr,ballgown-method Man page
exprfilter Man page
geneIDs Man page
geneIDs,ballgown-method Man page
geneNames Man page
geneNames,ballgown-method Man page
getAttributeField Man page
getGenes Man page
gexpr Man page
gexpr,ballgown-method Man page
gffRead Man page
gffReadGR Man page
iexpr Man page
iexpr,ballgown-method Man page
indexes Man page
indexes<- Man page
indexes<-,ballgown-method Man page
indexes,ballgown-method Man page
last Man page
mergedDate Man page
mergedDate,ballgown-method Man page
pctOverlap Man page
pData Man page
pData<- Man page
pData<-,ballgown,ANY-method Man page
pData,ballgown-method Man page
plotLatentTranscripts Man page
plotMeans Man page
plotTranscripts Man page
sampleNames Man page
sampleNames,ballgown-method Man page
seqnames Man page
seqnames,ballgown-method Man page
stattest Man page
structure Man page
structure,ballgown-method Man page
subset Man page
subset,ballgown-method Man page
texpr Man page
texpr,ballgown-method Man page
tGene Man page
transcriptIDs Man page
transcriptIDs,ballgown-method Man page
transcriptNames Man page
transcriptNames,ballgown-method Man page
writeFiles Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
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
build
build/vignette.rds
data
data/bg.rda
inst
inst/doc
inst/doc/ballgown.R
inst/doc/ballgown.Rmd
inst/doc/ballgown.html
inst/extdata
inst/extdata/annot.gtf.gz
inst/extdata/hg19_genes_small.gtf.gz
inst/extdata/sample01
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
tablemaker
tablemaker/tablemaker-2.1.1
tablemaker/tablemaker-2.1.1/build-aux
tablemaker/tablemaker-2.1.1/src
tablemaker/tablemaker-2.1.1/src/lemon
tablemaker/tablemaker-2.1.1/src/lemon/bits
tablemaker/tablemaker-2.1.1/src/lemon/concepts
tablemaker/tablemaker-2.1.1/src/locfit
tests
tests/test-all.R
tests/testthat
tests/testthat/test-annotation.R tests/testthat/test-constructor.R tests/testthat/test-plots.R tests/testthat/test-stats.R
vignettes
vignettes/ballgown.Rmd

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