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C

rareprob2

2 1
Identifying significantly deleterious variants from germline variation and somatic mutational events

calc-roi-covg

1 4
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.

C++

msisensor

95 40
microsatellite instability detection using tumor only or paired tumor-normal data

bassovac

4 2
Improved Bayesian inversion somatic caller

pindel2

2 2
Detecting break points of large deletions and medium sized insertions from paired-end short read

gclust

0 1
Microbial and Viral genome sequence clustering tool

pindel

0 1
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

Pindel2BAM

0 4
Convert Pindel data into SAM & BAM formats.

polyscape

0 2
Homopolymer and microsatellite analysis tool

Common Workflow Language

TinDaisy

3 1
CWL version of SomaticWrapper

tin-daisy

1 1
CWL version of SomaticWrapper

TinJasmine

0 0
CWL germline variant caller

vcf2maf-CWL

0 0
CWL wrapper around vcf2maf

Dockerfile

dockers

0 2

HTML

HTAN_bulkRNA_expression

0 0
pipeline for HTAN bulk RNA-Seq data quantification

Java

3d-portal

0 0
3D proximity visulization portal

JavaScript

hotspot3d_portal

2 3

Jupyter Notebook

pollock

0 1
A tool that classifies cells based on their gene expression

PHP

GenomeVIP

15 5

Perl

MuSiC2

45 22
identifying mutational significance in cancer genomes

hotspot3d

34 21
3D hotspot mutation proximity analysis tool

somaticwrapper

6 2
Detect somatic variants from tumor and normal exome data

misplice

4 5
Discover Mutation Induced Splice Sites

neoscan

2 1
predict neoantigen for indel and snvs

VirusScan

2 6
VirusScan Pipeline

LR-PKD

1 0
Analysis pipeline for haplotype-based variant detection

parse-kegg

1 6
Script to format KEGG pathway data for PathScan

proximity_3D

1 0
3D mutation proximity analysis tool

squaredancer

1 0
SV Detection for soft-clipped genomic or cDNA reads

VEP_annotate

1 0
CWL wrapper for VEP annotation

VirusIntegrate

1 0
Detect Virus integration site

10Xmapping

0 2
mapping somatic variants to cell barcodes in scRNA-Seq data

bassovacmate

0 0
a wrapper for Bassovac tool

COCOONS

0 0
COrrecting CO-Occuring multi-Nucleotide variation

germlinewrapper

0 2
detect germline variants from normal samples

misplice_gcloud

0 1

MouseFilter

0 0

MouseTrap2

0 0
A better mouse filter

parse-cosmic

0 1
Script to carefully parse through and standardize somatic variant lists from COSMIC

PepScan

0 0
Detect variants from mass spectra data

runcleaner

0 0
clean somaticwrapper and germlinewrapper run

SpliceInator_Public

0 0
SpliceInator

TinDaisy-Core

0 1
Core somatic caller scripts based on SomaticWrapper CWL branch

TinDaisy-VEP

0 0
CWL wrapper for VEP annotation

vcf2maf

0 1
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

Python

CharGer

65 29
Characterization of Germline variants

germline_variant_snakemake

5 0
Snakemake workflow to call germline variant

birdseed2vcf

1 6
Convert birdseed variant file with genotypes to a VCF file

BioMine

0 2
Bioinformatics data-mining

CPTAC3_splicing

0 1
CPTAC3 RNA-seq splicing pipeline

CPTAC_miRNA

0 0
miRNA sequencing analysis for CPTAC

cptac_rna_expression

0 0
CPTAC RNA expression pipeline

dnp_filter

0 0

fuscia

0 0
Detection of chimeric transcripts (aka fusions) from barcoded single cell RNA-seq

mnp_filter

0 0

pvacseq_msi

0 0
Identify immunogenic indels from MSIsensor output

VLD_FilterVCF

0 0
CWL implementation of VCF filter for variant VAF, length, read depth, and allelic depth

XHMM_germlineCNV

0 1
A Snakemake workflow to call germline copy number variants (CNVs) from whole-exome sequencing data.

R

PanCanAtlasGermline

29 14

gatk4wxscnv

5 1
Pipeline for WXS CNV using GATK4

griffin-fusion

2 0
Suite of fusion gene analysis tools

MIRMMR

2 4
Microsatellite Instability Regression using Methylation and Mutations in R

cptac_methylation

1 3
Methylation array analysis pipeline for CPTAC

mc3_icgc_variant_pipeline

1 1
Variant analysis pipeline to compare the public PCAWG and MC3 mutation files generated by ICGC and TCGA

phosphoproteomics

1 0
Directory hosting scripts used for phosphoproteomics analysis.

BreakPointSurveyor-Core

0 0

ccRCC_single_cell

0 0

ccRCC_snRNA_analysis

0 2

HotPho_Analysis

0 1
HotPho, a bioinformatics tool to discover spatially interacting phosphorylation sites and mutations in cancer

outlier

0 3
Outlier analysis module to identify aberrantly highly expressed genes.

phospho-signaling

0 0

SomaticHaplotype

0 0
Object-oriented tools for phase set analysis and somatic mutation phasing using linked-read WGS

RMarkdown

gdc_qc_analysis

2 3
Somatic mutation pipeline comparison of TCGA samples between Genomic Data Commons (GDC) and MC3

Shell

BreakPointSurveyor

18 3
A comprehensive pipeline to analyze and visualize structural variants

VariantQC

5 6
Variant quality checking scripts.

CPTAC3-RNA-related-pipeline

3 3
Gene/transcript expression; Fusion; de novo assembly

SomaticSV

3 1
CWL wrapper for Manta 1.4.0 and simple filter

somatic_sv_workflow

2 1

BICSEQ2

1 1
BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA

CPTAC3.catalog

1 1
Details about CPTAC3 data at GDC and in Ding Lab

CPTAC3_QC

1 0
Comprehensive QC of CPTAC3 sequence data

FASTQtoBAM

1 0
Automatic FASTQ to BAM pipeline (regular WES/WGS, 10x WES/WGS)

PDXToolkit

1 0

varscan_vcf_remap

1 0
Modify fields of Varscan VCF files. CWL implementation

VEP_Filter

1 0
TinDaisy modules for filtering VCF based on VEP annotation

CPTAC3.case.discover

0 1
Obtain submitted reads and clinical info associated with CPTAC3 cases

CromwellRunner

0 0
Scripts for managing Cromwell workflows

discover.CPTAC3.b1

0 0
Obtain download information for CPTAC3 Batch 1 genomic analysis

exportGDC

0 0
Utilities to copy GDC-controlled BamMap data across systems

FSAudit

0 0
Filesystem audit visualization

GATK_GermlineCaller

0 0
CWL tool for calling germline variants using GATK

GermlineWrapper.workflow

0 0
Workflow for GermlineWrapper project

HotspotFilter

0 0
CWL implementation of filter which merges VCFs according to BED file

importGDC

0 0
Command line client for Genomic Data Commons data downloads

importGDC.CPTAC3

0 0
Automated download of CPTAC3 data from GDC

importGDC.CPTAC3.b1

0 0
Download CPTAC3 Batch 1 data on MGI and DC2

MergeFilterVCF

0 0
CWL project for VCF merge and filter tool

Pindel_GermlineCaller

0 0
CWL project with Pindel germline calling and filtering

queryGDC

0 0
Command line client for Genomic Data Commons graphGL queries

RegulatoryGermline

0 1

SnpIndelProximityFilter

0 0
Flag all SNP variants within a given distance of an indel

SomaticWrapper.CPTAC3.b1

0 0
Driver scripts for CPTAC3 Batch 1 SomaticWrapper analyses

SomaticWrapper.workflow

0 0
Simple workflow implementation for SomaticWrapper on MGI and standard Docker environments

submit.CPTAC3

0 1
Scripts for submission of CPTAC3 data

Toolkit

0 0

Varscan_GermlineCaller

0 0
CWL implementation of Varscan Germline Caller

WUDocker

0 1
Utilities for launching docker in various Washington University environments