Files in GoekeLab/proActiv

Estimate Promoter Activity from RNA-Seq data

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

LICENSE.md

NAMESPACE

NEWS

R/PromoterAnnotation-class.R R/annotation-data-helper.R R/annotation-data.R R/data.R R/deprecated.R R/estimate-promoter-activity.R R/identify-alternative-promoters.R R/junction-read-count.R R/plot-proActiv.R R/proActiv.R R/reexports.R README.Rmd README.md

_pkgdown.yml

data/promoterAnnotation.gencode.v34.subset.rda

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/articles/index.html

docs/articles/proActiv.html

docs/articles/proActiv_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/proActiv_files/figure-html/Boxplot-1.png

docs/articles/proActiv_files/figure-html/VizAlternativePromoters txdb-1.png

docs/articles/proActiv_files/figure-html/VizMajorGeneExp-1.png

docs/articles/proActiv_files/figure-html/VizMajorMinorPosition-1.png

docs/articles/proActiv_files/figure-html/VizPromoterCategories-1.png

docs/articles/proActiv_files/figure-html/VizTsne-1.png

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/docsearch.json

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/PromoterAnnotation-class.html

docs/reference/Rplot001.png

docs/reference/boxplotPromoters.html

docs/reference/calculateJunctionReadCounts.html

docs/reference/calculatePromoterReadCounts.html

docs/reference/figures/proActiv_design.png

docs/reference/figures/proActiv_logoName.png

docs/reference/figures/proActiv_name.png

docs/reference/getAbsolutePromoterActivity.html

docs/reference/getAlternativePromoters.html

docs/reference/getGeneExpression.html

docs/reference/getRelativePromoterActivity.html

docs/reference/index.html

docs/reference/integrateProactiv.html

docs/reference/normalizePromoterReadCounts.html

docs/reference/plotHeatmap.html

docs/reference/plotPCA.html

docs/reference/preparePromoterAnnotation.html

docs/reference/proActiv.html

docs/reference/promoterAnnotation.gencode.v19.html

docs/reference/promoterAnnotation.gencode.v34.html

docs/reference/promoterAnnotation.gencode.v34.subset.html

docs/reference/promoterAnnotation.gencode.vM1.html

docs/reference/promoterAnnotation.gencode.vM25.html

docs/reference/reexports.html

docs/sitemap.xml

inst/CITATION

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

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

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

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

inst/extdata/vignette/junctions/SGNEx_A549_Illumina_replicate1-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_HepG2_Illumina_replicate2-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_HepG2_Illumina_replicate5-run1.subset.SJ.out.tab.gz

man/PromoterAnnotation-class.Rd man/boxplotPromoters.Rd man/calculateJunctionReadCounts.Rd man/calculatePromoterReadCounts.Rd

man/figures/proActiv_design.png

man/figures/proActiv_logoName.png

man/figures/proActiv_name.png

man/getAbsolutePromoterActivity.Rd man/getAlternativePromoters.Rd man/getGeneExpression.Rd man/getRelativePromoterActivity.Rd man/integrateProactiv.Rd man/normalizePromoterReadCounts.Rd man/plotHeatmap.Rd man/plotPCA.Rd man/preparePromoterAnnotation.Rd man/proActiv.Rd man/promoterAnnotation.gencode.v34.subset.Rd man/reexports.Rd

tests/figs/deps.txt

tests/figs/plotpromoters/plotpromoters.svg

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

vignettes/.gitignore

vignettes/proActiv.Rmd

GoekeLab/proActiv documentation built on Jan. 30, 2022, 3:52 a.m.