Files in pachterlab/kma
KeepMeAround: Intron Retention Detection in RNA-Seq data
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/IntronRetention.R
R/filters.R
R/import.R
R/misc_funcs.R
R/readWrite.R
R/testing.R
R/zero_coverage.R
README.md
inst/doc/kma.R
inst/doc/kma.Rmd
inst/doc/kma.html
inst/example/annotation/refGene_sf3b1.gtf
inst/example/annotation/sf3b1.fa
inst/example/annotation/sf3b1_with_introns.fa
inst/example/experiment/ortho/ortho1/xprs_out/results.xprs
inst/example/experiment/ortho/ortho1/zero_coverage.txt
inst/example/experiment/ortho/ortho2/xprs_out/results.xprs
inst/example/experiment/ortho/ortho2/zero_coverage.txt
inst/example/experiment/ortho/ortho3/xprs_out/results.xprs
inst/example/experiment/ortho/ortho3/zero_coverage.txt
inst/example/kma_pre-process_out/intron_to_transcripts.txt
inst/example/kma_pre-process_out/introns.bed
inst/example/kma_pre-process_out/introns.fa
inst/kma-kallisto.zip
inst/pre-process/README.md
inst/pre-process/generate_introns.py
inst/pre-process/gtf_parser.py
inst/pre-process/intron_ops.py
inst/pre-process/tests/inputs/GTF2IRD2.gtf
inst/pre-process/tests/inputs/SRSF2.gtf
inst/pre-process/tests/inputs/refGene_07.23.2014_CHL1.gtf
inst/pre-process/tests/inputs/refGene_07.23.2014_CLK1.gtf
inst/pre-process/tests/test_intron_ops.py
inst/pre-process/zeroCoverage.py
man/check_groupings.Rd
man/filter_low_frags.Rd
man/filter_low_tpm.Rd
man/filter_perfect_psi.Rd
man/getCol.Rd
man/get_batch_intron_zc.Rd
man/get_intron_zc.Rd
man/intron_length.Rd
man/intron_null_dist.Rd
man/melt_intron_coords.Rd
man/newIntronRetention.Rd
man/print.IntronRetention.Rd
man/retention_test.Rd
man/summarize_zero_coverage.Rd
tests/testthat.R
tests/testthat/test-IntronRetention.R
tests/testthat/test-filters.R
tests/testthat/test-readWrite.R
vignettes/kma.Rmd
