R/SourceData.R

In elmerfer/ArribaR: gene Expression quantification, Gene Fusion detection and Immuno Content Deconvolution by STAR and ARRIBA softwares

# ASSEMBLIES< - c(hs37d5="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz",
#                 hg19 ="http://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/chromFa.tar.gz",
#                 GRCh37="ftp://ftp.ensembl.org/pub/grch37/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz",
#                 hg38="http://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.chromFa.tar.gz",
#                 GRCh38="ftp://ftp.ensembl.org/pub/release-93/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz",
#                 mm10="http://hgdownload.cse.ucsc.edu/goldenpath/mm10/bigZips/chromFa.tar.gz",
#                 GRCm38="ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz")
#                 
# ANNOTATIONS <- c(GENCODE19="ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz",
#                  RefSeq_hg19="http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/refGene.txt.gz",
#                  ENSEMBL87="ftp://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.chr.gtf.gz",
#                  GENCODE28="ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.annotation.gtf.gz",
#                  RefSeq_hg38="http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/refGene.txt.gz",
#                  ENSEMBL93="ftp://ftp.ensembl.org/pub/release-93/gtf/homo_sapiens/Homo_sapiens.GRCh38.93.chr.gtf.gz",
#                  GENCODEM25="ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.annotation.gtf.gz",
#                  RefSeq_mm10="http://hgdownload.cse.ucsc.edu/goldenpath/mm10/database/refGene.txt.gz")