match assembled transcripts to annotated transcripts
Ballgown
constructor function for ballgown objects
The ballgown package for analysis of transcript assemblies
load RSEM data into a ballgown object
Toy ballgown object
plot annotated and assembled transcripts together
group a gene's assembled transcripts into clusters
cluster a gene's transcripts and calculate cluster-level expression
determine if one set of GRanges fully contains any of another set of GRanges
extract paths to tablemaker output
extract exon-level expression measurements from ballgown objects
Replacement method for expr slot in ballgown objects
extract expression components from ballgown objects
subset ballgown objects using an expression filter
get gene IDs from a ballgown object
get gene names from a ballgown object
extract a specific field of the "attributes" column of a data frame created from a GTF/GFF file
label assembled transcripts with gene names
extract gene-level expression measurements from ballgown objects
read in GTF/GFF file as a data frame
read in gtf file as GRanges object
extract transcript-level expression measurements from ballgown objects
Replace method for indexes slot in ballgown objects
extract the indexes from ballgown objects
get the last element
extract package version & creation date from ballgown object
Replacement method for pData slot in ballgown objects
extract phenotype data from a ballgown object
calculate percent overlap between two GRanges objects
cluster assembled transcripts and plot the results
visualize transcript abundance by group
visualize structure of assembled transcripts
get names of samples in a ballgown objects
get sequence (chromosome) names from ballgown object
statistical tests for differential expression in ballgown
extract structure components from ballgown objects
subset ballgown objects to specific samples or genomic locations
Connect a transcript to its gene
extract transcript-level expression measurements from ballgown objects
get numeric transcript IDs from a ballgown object
get transcript names from a ballgown object
write files to disk from ballgown object