proactivWorkflow: Identifying active and alternative promoters from RNA-Seq data with proActiv

This data set comprises one tar file containing all files necessary for the running of the proactivWorkflow package. RDS files corresponding to promoter annotations for GENCODE v19 and v34 are provided for direct loading into R.

Directory TCGA_Kidney_Junction_Files contains processed junction files (BED) of KIRC normal and tumour samples (Source: The Cancer Genome Atlas Research Network, https://portal.gdc.cancer.gov/)

Directory Yan_Junction_Files contains processed junction files (BED) of human preimplantation embryos and human embryonic stem cells (Raw sequencing data: GSE36552, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36552)

gencode.v19.annotation.gtf: GENCODE annotations (Human Release 19) 
(Source: GENCODE, https://www.gencodegenes.org/human/release_19.html)  

gencode.v34.annotation.gtf: GENCODE annotations (Human Release 34)  
(Source: GENCODE, https://www.gencodegenes.org/human/release_34.html)

condition.tcga.rds: a character vector of the conditions for each KIRC sample  

condition.yan.rds: a character vector of the conditions for each embryo sample  

junctionFilePaths.tcga.rds: a character vector of the junction file paths for each KIRC sample

junctionFilePaths.yan.rds: a character vector of the junction file paths for each embryo sample

promoterAnnotation.gencodev19.rds: promoter annotation object corresponding to GENCODE annotation (Human Release 19)  

promoterAnnotation.gencodev34.rds: promoter annotation object corresponding to GENCODE annotation (Human Release 34)