id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-003045-r707jl16	Bhuvaneshwar, Krithika	viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors	2018-06-05		.txt	text/plain	6546	359	54	The pipeline includes 4 major modules: The first module aligns and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral-gene level thus allowing for downstream differential expression analysis of viral genes between case and controls groups. Available online at: https:// www.fda.gov/biologicsbloodvaccines/bloodbloodproducts/approvedproducts/ licensedproductsblas/blooddonorscreening/infectiousdisease/ucm080466.htm Abbreviations: HBV, Hepatitis B virus; HCV, Hepatitis C Virus; HERV K113, Human Endogenous Retrovirus K113; TCGA, The Cancer Genome Atlas; HCC, Hepatocellular carcinoma; NAFLD, nonalcoholic fatty liver disease; Hep B, Hepatitis B; Hep C, Hepatitis C; HepB + HepC, coinfected with both Hepatitis B and C virus; HBsAg, Hepatitis B surface antigen; HBeAg, Hepatitis B type e antigen; NGS, next-generation sequencing; RNA-seq, whole transcriptome sequencing; BAM, Binary version of Sequence alignment/map format; CDS, coding sequence; Cox PH, Cox Proportional Hazard; HBx, viral gene X; STS, Sequence-tagged sites; NCBI, National Center for Biotechnology Information; GFF, general-feature-format.	./cache/cord-003045-r707jl16.txt	./txt/cord-003045-r707jl16.txt