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

This data set comprises all files necessary for the running of the proactivWorkflow package. 

• Embryos_Junction_Files.tar.gz: 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)
• LUAD_Junction_Files.tar.gz: processed junction files (BED) of Lung Adenocarcinoma normal (n=20) and tumour (n=20) samples (TCGA)
  (Source: The Cancer Genome Atlas Research Network, https://portal.gdc.cancer.gov/)
• LUSC_Junction_Files.tar.gz: processed junction files (BED) of Lung Squamous Cell Carcinoma normal (n=20) and tumour (n=20) samples (TCGA)
  (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)  
• promoterAnnotation.gencodev19.rds: promoter annotation object corresponding to GENCODE annotation (Human Release 19)  
• resEmbryo.rds: proActiv SummarizedExperiment object of embryo samples
• resLUAD.rds: proActiv SummarizedExperiment object of LUAD samples
• resLUSC.rds: proActiv SummarizedExperiment object of LUSC samples
• resLUNG.rds: proActiv SummarizedExperiment object of LUAD and LUSC samples