ballgown: Flexible, isoform-level differential expression analysis

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

Author
Jack Fu [aut], Alyssa C. Frazee [aut, cre], Leonardo Collado-Torres [aut], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Date of publication
None
Maintainer
Jack Fu <jmfu@jhsph.edu>
License
Artistic-2.0
Version
2.6.0

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