NCI-Cancer Genomics Research Lab/FNLCR

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65 repositories

ONT_Analysis_Xin_Share_Pubic
Public template
HTML
•0•0•0•0•Updated Oct 16, 2025Oct 16, 2025
TriosCompass_v2
Public
Trios analysis workflow written in Snakemake
HTML
•
MIT License
•0•3•1•1•Updated Oct 8, 2025Oct 8, 2025
TypeSeq2
Public
R
•0•1•1•0•Updated Sep 10, 2025Sep 10, 2025
ExomeQcPipeline
Public
Python
•1•0•3•0•Updated Aug 20, 2025Aug 20, 2025
GEMSCAN
Public
Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.
workflow snakemake variant-calling deepvariant strelka2 gatk4-haplotypecaller
Python
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MIT License
•9•7•16•0•Updated Aug 18, 2025Aug 18, 2025
CGR_pacbio_hpylori_analysis_pipeline
Public
Shell
•0•0•0•0•Updated Aug 18, 2025Aug 18, 2025
GwasQcPipeline
Public
The CGR GWAS QC processing workflow.
gwas snakemake plink cancer-genomics illumina-bead-chip
Python
•
Other
•2•0•20•0•Updated Aug 8, 2025Aug 8, 2025
QIIME_pipeline
Public
CGR's QIIME microbiome pipeline
Python
•
MIT License
•3•4•1•0•Updated Jul 24, 2025Jul 24, 2025
AutoGVP_Snakemake_Workflow
Public
Python
•
MIT License
•0•0•1•0•Updated May 30, 2025May 30, 2025
AutoGVP
Public
R
•5•0•1•0•Updated Apr 1, 2025Apr 1, 2025
HPV_Guanacaste_CostaRica_Longitudinal_Study
Public
Includes the variant calling pipeline and data for the HPV natural history study
Python
•
MIT License
•0•0•0•0•Updated Mar 24, 2025Mar 24, 2025
MineSV
Public
Python
•
GNU General Public License v3.0
•0•0•4•0•Updated Mar 6, 2025Mar 6, 2025
ITSxpress-docs
Public
0•0•0•0•Updated Feb 24, 2025Feb 24, 2025
GenCompass_WGS
Public
GenCompass: Germline Ensemble Calling of Mutations with Parabricks Accelerated Software Suite
WDL
•0•1•0•0•Updated Nov 20, 2024Nov 20, 2024
GwasQcPipeline-test-data
Public
Fake test data sets for the GwasQcPipeline.
Shell
•0•0•0•0•Updated Sep 24, 2024Sep 24, 2024
ImpureMerge
Public
Python
•0•0•0•0•Updated Sep 24, 2024Sep 24, 2024
PreImputePipeline
Public
PreImputePipeline
C++
•1•1•1•0•Updated Jul 25, 2024Jul 25, 2024
gatk-sv
Public
A structural variation pipeline for short-read sequencing - modified to run on HPC
Python
•
BSD 3-Clause "New" or "Revised" License
•77•1•1•0•Updated May 28, 2024May 28, 2024
UKB_extract_variants
Public
Extract variants of interest from UKB Biobank data hosted at DNAnexus
Perl
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MIT License
•0•0•0•0•Updated Apr 30, 2024Apr 30, 2024
conda-cgr
Public
CGR conda channel
HTML
•1•2•3•0•Updated Apr 25, 2024Apr 25, 2024
HPV_low_VAF_SNV_prediction
Public
Predicting true low-VAF SNVs in HPV using triplicate NGS samples and machine learning
machine-learning vcf cancer-genomics variant-calling snv vcf-files ngs-analysis hpv ion-torrent variant-call-format
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Mar 12, 2024Mar 12, 2024
Gencode_microRNA-seq
Public
microRNA-seq workflow utilizing STAR to generate a Sample-Gene read count matrix
Python
•
Creative Commons Zero v1.0 Universal
•0•0•6•0•Updated Jan 5, 2024Jan 5, 2024
IlluminaSequencingAnalysis
Public
All Illumina Sequencing Related project from Xin will be recorded in this repo
Shell
•0•0•60•0•Updated Dec 21, 2023Dec 21, 2023
igv_snapshot_maker
Public
Perl
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MIT License
•0•0•0•0•Updated Sep 20, 2023Sep 20, 2023
HPVMethyl
Public
R
•0•0•0•0•Updated Jun 26, 2023Jun 26, 2023
TypeSeqHPV
Public
NCI CGR laboratory HPV typing analysis workflows
docker r tidyverse ion-torrent-plugin torrent-server
R
•4•5•0•0•Updated Dec 15, 2022Dec 15, 2022
somatic-conda
Public
This is a full snakemake pipeline for somatic-combiner.
Python
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MIT License
•0•0•0•0•Updated Sep 20, 2022Sep 20, 2022
annotate_rsids_from_linker
Public
Use linker file to map chr:pos to rsID labels, for plco-analysis
M4
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MIT License
•0•0•0•0•Updated Jan 16, 2022Jan 16, 2022
annotate_frequency
Public
Annotate plco-analysis intermediate files with frequency data
M4
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MIT License
•0•0•0•0•Updated Dec 24, 2021Dec 24, 2021
RNA_CGR_Pipeline
Public
The RNA pipeline developed by Mia and Xin, including RNA analysis pipeline and RNA auto-launcher
Python
•
MIT License
•1•0•0•0•Updated Dec 14, 2021Dec 14, 2021