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
