Package: ballgown 2.39.0

Jack Fu

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.

Authors:Jack Fu [aut], Alyssa C. Frazee [aut, cre], Leonardo Collado-Torres [aut], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]

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ballgown.pdf |ballgown.html✨
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NEWS

# Install 'ballgown' in R:
install.packages('ballgown', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/alyssafrazee/ballgown/issues

Datasets:
  • bg - Toy ballgown object

On BioConductor:ballgown-2.39.0(bioc 3.21)ballgown-2.38.0(bioc 3.20)

immunooncologyrnaseqstatisticalmethodpreprocessingdifferentialexpression

10.49 score 142 stars 1 packages 334 scripts 1.8k downloads 21 mentions 40 exports 80 dependencies

Last updated 2 months agofrom:01a0bbb9d9. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:annotate_assemblyballgownballgownrsemcheckAssembledTxclusterTranscriptscollapseTranscriptscontainsdirseexprexprexpr<-exprfiltergeneIDsgeneNamesgetAttributeFieldgetGenesgexprgffReadgffReadGRiexprindexesindexes<-lastmergedDatepctOverlappDatapData<-plotLatentTranscriptsplotMeansplotTranscriptssampleNamesseqnamesstatteststructuresubsettexprtGenetranscriptIDstranscriptNameswriteFiles

Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayedgeRfastmapformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpkgconfigplogrpngR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystatmodSummarizedExperimentsurvivalsvasysUCSC.utilsvctrsXMLxtableXVectoryamlzlibbioc

Flexible isoform-level differential expression analysis with Ballgown

Rendered fromballgown.Rmdusingknitr::knitron Nov 29 2024.

Last update: 2018-08-28
Started: 2014-07-28

Readme and manuals

Help Manual

Help pageTopics
The ballgown package for analysis of transcript assembliesballgown-package ballgownp
match assembled transcripts to annotated transcriptsannotate_assembly
BallgownBallgown ballgown-class
constructor function for ballgown objectsballgown ballgown-constructor
load RSEM data into a ballgown objectballgownrsem
Toy ballgown objectbg
plot annotated and assembled transcripts togethercheckAssembledTx
group a gene's assembled transcripts into clustersclusterTranscripts
cluster a gene's transcripts and calculate cluster-level expressioncollapseTranscripts
determine if one set of GRanges fully contains any of another set of GRangescontains
extract paths to tablemaker outputdirs dirs,ballgown-method
extract exon-level expression measurements from ballgown objectseexpr eexpr,ballgown-method
extract expression components from ballgown objectsexpr expr,ballgown-method
Replacement method for expr slot in ballgown objectsexpr<- expr<-,ballgown-method
subset ballgown objects using an expression filterexprfilter
get gene IDs from a ballgown objectgeneIDs geneIDs,ballgown-method
get gene names from a ballgown objectgeneNames geneNames,ballgown-method
extract a specific field of the "attributes" column of a data frame created from a GTF/GFF filegetAttributeField
label assembled transcripts with gene namesgetGenes
extract gene-level expression measurements from ballgown objectsgexpr gexpr,ballgown-method
read in GTF/GFF file as a data framegffRead
read in gtf file as GRanges objectgffReadGR
extract transcript-level expression measurements from ballgown objectsiexpr iexpr,ballgown-method
extract the indexes from ballgown objectsindexes indexes,ballgown-method
Replace method for indexes slot in ballgown objectsindexes<- indexes<-,ballgown-method
get the last elementlast
extract package version & creation date from ballgown objectmergedDate mergedDate,ballgown-method
calculate percent overlap between two GRanges objectspctOverlap
extract phenotype data from a ballgown objectpData pData,ballgown-method
Replacement method for pData slot in ballgown objectspData<- pData<-,ballgown,ANY-method
cluster assembled transcripts and plot the resultsplotLatentTranscripts
visualize transcript abundance by groupplotMeans
visualize structure of assembled transcriptsplotTranscripts
get names of samples in a ballgown objectssampleNames sampleNames,ballgown-method
get sequence (chromosome) names from ballgown objectseqnames seqnames,ballgown-method
statistical tests for differential expression in ballgownstattest
extract structure components from ballgown objectsstructure structure,ballgown-method
subset ballgown objects to specific samples or genomic locationssubset subset,ballgown-method
extract transcript-level expression measurements from ballgown objectstexpr texpr,ballgown-method
Connect a transcript to its genetGene
get numeric transcript IDs from a ballgown objecttranscriptIDs transcriptIDs,ballgown-method
get transcript names from a ballgown objecttranscriptNames transcriptNames,ballgown-method
write files to disk from ballgown objectwriteFiles