Pinned Repositories
cgrHPV16
ChernobylDNMCalling
Code for calling de novo mutations in Chernobyl trios.
ChernobylThyroidCancer-Clustering
GEMSCAN
Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.
MoCCA-SV
A Flexible Ensemble Framework for Structural Variant Analysis
Pacbio-Alternative-Splicing
PING_BIOWULF
A workflow to run PING (Pushing Immunogenetics to the Next Generation) efficiently on NIH Biowulf
plco-analysis
Primary workflow for the PLCO "Atlas" project
QIIME_pipeline
CGR's QIIME microbiome pipeline
TypeSeqHPV
NCI CGR laboratory HPV typing analysis workflows
NCI-Cancer Genomics Research Lab/FNLCR's Repositories
NCI-CGR/GEMSCAN
Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.
NCI-CGR/TypeSeqHPV
NCI CGR laboratory HPV typing analysis workflows
NCI-CGR/QIIME_pipeline
CGR's QIIME microbiome pipeline
NCI-CGR/plco-analysis
Primary workflow for the PLCO "Atlas" project
NCI-CGR/conda-cgr
CGR conda channel
NCI-CGR/PING_BIOWULF
A workflow to run PING (Pushing Immunogenetics to the Next Generation) efficiently on NIH Biowulf
NCI-CGR/TypeSeq2
NCI-CGR/GwasQcPipeline
The CGR GWAS QC processing workflow.
NCI-CGR/annotate_frequency
Annotate plco-analysis intermediate files with frequency data
NCI-CGR/annotate_rsids_from_linker
Use linker file to map chr:pos to rsID labels, for plco-analysis
NCI-CGR/CGR_pacbio_hpylori_analysis_pipeline
NCI-CGR/COVNET-GWAS
COVNET GWAS pipeline developement
NCI-CGR/ExomeQcPipeline
NCI-CGR/gatk-sv
A structural variation pipeline for short-read sequencing - modified to run on HPC
NCI-CGR/Gencode_microRNA-seq
microRNA-seq workflow utilizing STAR to generate a Sample-Gene read count matrix
NCI-CGR/GenCompass_WGS
GenCompass: Germline Ensemble Calling of Mutations with Parabricks Accelerated Software Suite
NCI-CGR/HPV_low_VAF_SNV_prediction
Predicting true low-VAF SNVs in HPV using triplicate NGS samples and machine learning
NCI-CGR/HPVMethyl
NCI-CGR/IGV_snapshot_automation
NCI-CGR/igv_snapshot_maker
NCI-CGR/IlluminaSequencingAnalysis
All Illumina Sequencing Related project from Xin will be recorded in this repo
NCI-CGR/MineSV
NCI-CGR/Nanopore_DNA-seq
NCI-CGR/Nanopore_Pore_C_Tips
NCI-CGR/Nanopore_RNA-seq
NCI-CGR/PLP_prediction_workflow
NCI-CGR/RNA_CGR_Pipeline
The RNA pipeline developed by Mia and Xin, including RNA analysis pipeline and RNA auto-launcher
NCI-CGR/somatic-conda
This is a full snakemake pipeline for somatic-combiner.
NCI-CGR/TriosCompass_v2
Trios analysis workflow written in Snakemake
NCI-CGR/UKB_extract_variants
Extract variants of interest from UKB Biobank data hosted at DNAnexus