Discover ding-lab/LR-PKD Open Source project

Characterization of Germline variants

121

CharGer

identifying mutational significance in cancer genomes

MuSiC2

3D hotspot mutation proximity analysis tool

hotspot3d

A comprehensive pipeline to analyze and visualize structural variants

PanCanAtlasGermline

GenomeVIP

PHP

BreakPointSurveyor

Detect somatic variants from tumor and normal WGS/WXS data

somaticwrapper

BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA

PanCan_snATAC_publication

Jupyter Notebook

BICSEQ2

Variant quality checking scripts.

VariantQC

call copy number from WES(WXS)

cnvkit_pipeline

Discover Mutation Induced Splice Sites

misplice

predict neoantigen for indel and snvs

neoscan

VirusScan

VirusScan Pipeline

Methylation array analysis pipeline for CPTAC

cptac_methylation

TinDaisy

CWL somatic variant caller

Common Workflow Language

gatk4wxscnv

Pipeline for WXS CNV using GATK4

germline_variant_snakemake

Snakemake workflow to call germline variant

Improved Bayesian inversion somatic caller

ccRCC_snRNA_analysis

bassovac

Detection of chimeric transcripts (aka fusions) from barcoded single cell RNA-seq

fuscia

Suite of fusion gene analysis tools

griffin-fusion

CPTAC3-RNA-related-pipeline

Gene/transcript expression; Fusion; de novo assembly

Variant analysis pipeline to compare the public PCAWG and MC3 mutation files generated by ICGC and TCGA

mc3_icgc_variant_pipeline

germlinewrapper

detect germline variants from normal samples

Convert birdseed variant file with genotypes to a VCF file

birdseed2vcf

Cohort DNA Copy Number Analysis

cmds

TinJasmine

CWL germline variant caller

Common Workflow Language

MIRMMR

Microsatellite Instability Regression using Methylation and Mutations in R

HotPho_Analysis

HotPho, a bioinformatics tool to discover spatially interacting phosphorylation sites and mutations in cancer

SomaticSV

CWL wrapper for Manta 1.4.0 and simple filter

miRNA sequencing analysis for CPTAC

CPTAC_miRNA

Automatic FASTQ to BAM pipeline (regular WES/WGS, 10x WES/WGS)

FASTQtoBAM

Script to format KEGG pathway data for PathScan

parse-kegg

infer_cnv_postprocesssing

Detecting break points of large deletions and medium sized insertions from paired-end short read

pindel2

Modify fields of Varscan VCF files. CWL implementation

varscan_vcf_remap

A tool that classifies cells based on their gene expression

pollock

Ancestry prediction from .bam files

ancestry

Jupyter Notebook

10Xmapping

mapping somatic variants to cell barcodes in scRNA-Seq data

Automated download of CPTAC3 data from GDC

importGDC

Given two BAM files, a reference sequence, and regions of interest, count the AT, CG, or CpG sites with sufficient read-depth in both BAMs.

calc-roi-covg

gdc_qc_analysis

Somatic mutation pipeline comparison of TCGA samples between Genomic Data Commons (GDC) and MC3

RMarkdown

hotspot3d_portal

JavaScript

VEP_Filter

TinDaisy modules for filtering VCF based on VEP annotation

Identifying significantly deleterious variants from germline variation and somatic mutational events

PDX-PanCanAtlas

Jupyter Notebook

rareprob2

TinDaisy-Core

Core somatic caller scripts based on SomaticWrapper CWL branch

Fusion_hg38

Convert Pindel data into SAM & BAM formats.

SalmonTE

Pindel2BAM

Directory hosting scripts used for phosphoproteomics analysis.

phosphoproteomics

PDXToolkit

CPTAC RNA expression pipeline

cptac_rna_expression

druggability_databases

CWL tool for calling germline variants using GATK

GATK_GermlineCaller

CWL wrapper for VEP annotation

VEP_annotate

Common Workflow Language

GDC.case.discover

Obtain submitted reads and clinical info associated with CPTAC3 cases

SV Detection for soft-clipped genomic or cDNA reads

phospho-signaling

squaredancer

Comprehensive QC of CPTAC3 sequence data

CPTAC3_QC

Detect Virus integration site

VirusIntegrate

Scripts for managing Cromwell workflows

CromwellRunner