Files in kauralasoo/txrevise
Extend and revise transcript annotatons.
.gitignore
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
R/addTranscriptAnnotations.R
R/classifyDifference.R
R/compareGRanges.R
R/constructAlternativeEvents.R
R/extendTruncatedTranscripts.R
R/helperFunctions.R
R/maskInternalExons.R
R/processEnsemblAnnotations.R
R/reviseAnnotations-package.r
README.md
build_container.sh
data/FRMD4B.rds
data/IRF5.rds
data/promoters.tsv
inst/doc/construct_events.R
inst/doc/construct_events.Rmd
inst/doc/construct_events.html
man/basesDifferent.Rd
man/calculateBasepairDifference.Rd
man/constructAlternativeEvents.Rd
man/constructAlternativeEventsWrapper.Rd
man/constructEventMetadata.Rd
man/dataFrameToGRanges.Rd
man/extendSingleTranscript.Rd
man/extendTranscriptsPerGene.Rd
man/extractGeneData.Rd
man/fillMissingInternalExons.Rd
man/filterTranscriptMetadata.Rd
man/flattenAlternativeEvents.Rd
man/identifyTranscriptGroups.Rd
man/importTranscriptMetadataFromGTF.Rd
man/indentifyAddedRemovedRegions.Rd
man/listIntersect.Rd
man/listUnion.Rd
man/makeGeneTranscriptFromExons.Rd
man/markLongestGencodeTranscript.Rd
man/mergeByMaxDifference.Rd
man/replaceExtendedTranscripts.Rd
man/reviseAnnotations.Rd
man/splitIntoBatches.Rd
man/transcriptsToAnnotations.Rd
scripts/Snakefile
scripts/build_cage_annotations.R
scripts/constructEvents.R
scripts/extractTranscriptTags.py
scripts/make_annotation_metadata.R
scripts/prepareAnnotations.R
scripts/prepare_CAGE_data.R
scripts/run_snakemake.sh
scripts/run_txrevise.sh
scripts/snakemake_submit_UT.py
tests/data/cdss_test.rds
tests/data/exons_test.rds
tests/data/treatment_res_annot.rds
tests/testthat.R
tests/testthat/constructSampleData.R
tests/testthat/testReviseAnnotations.R
vignettes/construct_events.Rmd
vignettes/tuQTL_analysis.md
