Files in Bioconductor/SplicingGraphs
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads
to them
.Rinstignore
DESCRIPTION
NAMESPACE
R/SplicingGraphs-class.R
R/assignReads.R
R/bubbles-methods.R
R/countReads-methods.R
R/igraph-utils.R
R/plotTranscripts-methods.R
R/rsgedgesByGene-methods.R
R/sgedges-methods.R
R/sgedgesByGene-methods.R
R/sgraph-methods.R
R/toy_data.R
R/txpath-methods.R
R/utils.R
R/zzz.R
README.md
TODO
inst/extdata/ASpatterns.txt
inst/extdata/TSPCsg.rda
inst/extdata/toy_genes.gff3
inst/extdata/toy_overlaps.txt
inst/extdata/toy_reads.sam
inst/scripts/TSPC-utils.R
inst/scripts/create-vignette-plots.R
inst/scripts/makeTSPCsg.R
inst/unitTests/test_countReads-methods.R
man/SplicingGraphs-class.Rd
man/SplicingGraphs-package.Rd
man/TSPCsg.Rd
man/assignReads.Rd
man/bubbles-methods.Rd
man/countReads-methods.Rd
man/plotTranscripts-methods.Rd
man/rsgedgesByGene-methods.Rd
man/sgedges-methods.Rd
man/sgedgesByGene-methods.Rd
man/sgraph-methods.Rd
man/toy_data.Rd
man/txpath-methods.Rd
tests/run_unitTests.R
vignettes/SplicingGraphs.Rnw
vignettes/images/CIB3-sg.pdf
vignettes/images/CIB3-sg2.pdf
vignettes/images/CIB3-transcripts.pdf
vignettes/images/ZNF813-sg.pdf
vignettes/images/ZNF813-sg2.pdf
vignettes/images/ZNF813-transcripts.pdf
vignettes/precomputed_results/sg_with_bubbles.rda
vignettes/precomputed_results/sg_with_reads.rda
