NCI-Cancer Genomics Research Lab/FNLCR's repositories
TypeSeqHPV
NCI CGR laboratory HPV typing analysis workflows
QIIME_pipeline
CGR's QIIME microbiome pipeline
plco-analysis
Primary workflow for the PLCO "Atlas" project
PING_BIOWULF
A workflow to run PING (Pushing Immunogenetics to the Next Generation) efficiently on NIH Biowulf
GwasQcPipeline
The CGR GWAS QC processing workflow.
annotate_frequency
Annotate plco-analysis intermediate files with frequency data
annotate_rsids_from_linker
Use linker file to map chr:pos to rsID labels, for plco-analysis
COVNET-GWAS
COVNET GWAS pipeline developement
gatk-sv
A structural variation pipeline for short-read sequencing - modified to run on HPC
Gencode_microRNA-seq
microRNA-seq workflow utilizing STAR to generate a Sample-Gene read count matrix
HPV_low_VAF_SNV_prediction
Predicting true low-VAF SNVs in HPV using triplicate NGS samples and machine learning
IlluminaSequencingAnalysis
All Illumina Sequencing Related project from Xin will be recorded in this repo
RNA_CGR_Pipeline
The RNA pipeline developed by Mia and Xin, including RNA analysis pipeline and RNA auto-launcher
somatic-conda
This is a full snakemake pipeline for somatic-combiner.
TriosCompass_v2
Trios analysis workflow written in Snakemake
UKB_extract_variants
Extract variants of interest from UKB Biobank data hosted at DNAnexus