Man pages for alyssafrazee/ballgown
Flexible, isoform-level differential expression analysis

annotate_assemblymatch assembled transcripts to annotated transcripts
ballgown-constructorconstructor function for ballgown objects
ballgown-packageThe ballgown package for analysis of transcript assemblies
ballgownrsemload RSEM data into a ballgown object
bgToy ballgown object
checkAssembledTxplot annotated and assembled transcripts together
clusterTranscriptsgroup a gene's assembled transcripts into clusters
collapseTranscriptscluster a gene's transcripts and calculate cluster-level...
containsdetermine if one set of GRanges fully contains any of another...
dirsextract paths to tablemaker output
eexprextract exon-level expression measurements from ballgown...
exprextract expression components from ballgown objects
exprfiltersubset ballgown objects using an expression filter
expr-replaceReplacement method for expr slot in ballgown objects
geneIDsget gene IDs from a ballgown object
geneNamesget gene names from a ballgown object
getAttributeFieldextract a specific field of the "attributes" column of a data...
getGeneslabel assembled transcripts with gene names
gexprextract gene-level expression measurements from ballgown...
gffReadread in GTF/GFF file as a data frame
gffReadGRread in gtf file as GRanges object
iexprextract transcript-level expression measurements from...
indexesextract the indexes from ballgown objects
indexes-replaceReplace method for indexes slot in ballgown objects
lastget the last element
mergedDateextract package version & creation date from ballgown object
pctOverlapcalculate percent overlap between two GRanges objects
pDataextract phenotype data from a ballgown object
pData-replaceReplacement method for pData slot in ballgown objects
plotLatentTranscriptscluster assembled transcripts and plot the results
plotMeansvisualize transcript abundance by group
plotTranscriptsvisualize structure of assembled transcripts
sampleNamesget names of samples in a ballgown objects
seqnamesget sequence (chromosome) names from ballgown object
statteststatistical tests for differential expression in ballgown
structureextract structure components from ballgown objects
subsetsubset ballgown objects to specific samples or genomic...
texprextract transcript-level expression measurements from...
tGeneConnect a transcript to its gene
transcriptIDsget numeric transcript IDs from a ballgown object
transcriptNamesget transcript names from a ballgown object
writeFileswrite files to disk from ballgown object
alyssafrazee/ballgown documentation built on May 11, 2017, 12:12 a.m.