Files in proActiv

Estimate Promoter Activity from RNA-Seq data

README.md

NEWS

NAMESPACE

DESCRIPTION

LICENSE

build/vignette.rds

data/promoterAnnotation.gencode.v34.subset.rda

R/PromoterAnnotation-class.R R/proActiv.R R/annotation-data-helper.R R/reexports.R R/junction-read-count.R R/plot-proActiv.R R/data.R R/estimate-promoter-activity.R R/annotation-data.R vignettes/proActiv.Rmd man/plotPromoters.Rd man/reexports.Rd man/calculateJunctionReadCounts.Rd man/PromoterAnnotation-class.Rd man/preparePromoterAnnotation.Rd man/promoterAnnotation.gencode.v34.subset.Rd man/getAbsolutePromoterActivity.Rd man/normalizePromoterReadCounts.Rd man/proActiv.Rd man/getRelativePromoterActivity.Rd man/calculatePromoterReadCounts.Rd man/getGeneExpression.Rd

man/figures/proActiv_design.png

man/figures/proActiv_logoName.png

man/figures/proActiv_name.png

tests/testthat.R tests/testthat/test_proActiv.R tests/testthat/test_annotation-data.R tests/testthat/test_plot-proActiv.R

tests/figs/deps.txt

tests/figs/plotpromoters/plotpromoters.svg

inst/CITATION

inst/doc/proActiv.html

inst/doc/proActiv.R inst/doc/proActiv.Rmd

inst/extdata/vignette/junctions/SGNEx_HepG2_Illumina_replicate2-run1.subset.SJ.out.tab.gz

inst/extdata/vignette/junctions/SGNEx_HepG2_Illumina_replicate5-run1.subset.SJ.out.tab.gz

inst/extdata/vignette/junctions/SGNEx_HepG2_Illumina_replicate4-run1.subset.SJ.out.tab.gz

inst/extdata/vignette/junctions/SGNEx_A549_Illumina_replicate3-run1.subset.SJ.out.tab.gz

inst/extdata/vignette/junctions/SGNEx_A549_Illumina_replicate5-run1.subset.SJ.out.tab.gz

inst/extdata/vignette/junctions/SGNEx_A549_Illumina_replicate1-run1.subset.SJ.out.tab.gz

inst/extdata/vignette/annotations/gencode.v34.annotation.rap1gap.sqlite

inst/extdata/vignette/annotations/exonsBy.rap1gap.rds

inst/extdata/vignette/annotations/gencode.v34.annotation.subset.gtf.gz

inst/extdata/vignette/annotations/gencode.v34.annotation.subset.sqlite

inst/extdata/testdata/bam/SGNEx_A549_Illumina_replicate1-run1_genome_subset.bam

inst/extdata/testdata/bam/SGNEx_MCF7_Illumina_replicate2-run1_genome_subset.bam

proActiv documentation built on Nov. 8, 2020, 8:14 p.m.