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rareprob2

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

92 37
microsatellite instability detection using tumor only or paired tumor-normal data

bassovac

4 2
Improved Bayesian inversion somatic caller

pindel2

1 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.
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

Dockerfile

dockers

0 2

Java

3d-portal

0 0
3D proximity visulization portal

JavaScript

Jupyter Notebook

pollock

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

PHP

GenomeVIP

15 5

Perl

MuSiC2

43 22
identifying mutational significance in cancer genomes

hotspot3d

33 20
3D hotspot mutation proximity analysis tool
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

LR-PKD

1 0
Analysis pipeline for haplotype-based variant detection
Script to format KEGG pathway data for PathScan
3D mutation proximity analysis tool
SV Detection for soft-clipped genomic or cDNA reads
Detect Virus integration site

VirusScan

1 6
VirusScan Pipeline
mapping somatic variants to cell barcodes in scRNA-Seq data
a wrapper for Bassovac tool

COCOONS

0 0
COrrecting CO-Occuring multi-Nucleotide variation
detect germline variants from normal samples
A better mouse filter
Script to carefully parse through and standardize somatic variant lists from COSMIC

PepScan

0 0
Detect variants from mass spectra data
clean somaticwrapper and germlinewrapper run
SpliceInator
Core somatic caller scripts based on SomaticWrapper CWL branch

vcf2maf

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

Python

CharGer

62 28
Characterization of Germline variants
Snakemake workflow to call germline variant
Convert birdseed variant file with genotypes to a VCF file

BioMine

0 2
Bioinformatics data-mining
CPTAC3 RNA-seq splicing pipeline
miRNA sequencing analysis for CPTAC
CPTAC RNA expression pipeline

fuscia

0 0
Detection of chimeric transcripts (aka fusions) from barcoded single cell RNA-seq
CWL implementation of VCF filter for variant VAF, length, read depth, and allelic depth
A Snakemake workflow to call germline copy number variants (CNVs) from whole-exome sequencing data.

R

Pipeline for WXS CNV using GATK4

MIRMMR

2 4
Microsatellite Instability Regression using Methylation and Mutations in R
Methylation array analysis pipeline for CPTAC
Suite of fusion gene analysis tools
Directory hosting scripts used for phosphoproteomics analysis.
HotPho, a bioinformatics tool to discover spatially interacting phosphorylation sites and mutations in cancer
Variant analysis pipeline to compare the public PCAWG and MC3 mutation files generated by ICGC and TCGA

outlier

0 3
Outlier analysis module to identify aberrantly highly expressed genes.
Object-oriented tools for phase set analysis and somatic mutation phasing using linked-read WGS

RMarkdown

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

Shell

A comprehensive pipeline to analyze and visualize structural variants

VariantQC

5 6
Variant quality checking scripts.
Gene/transcript expression; Fusion; de novo assembly

SomaticSV

2 1
CWL wrapper for Manta 1.4.0 and simple filter

BICSEQ2

1 1
BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA
Details about CPTAC3 data at GDC and in Ding Lab

CPTAC3_QC

1 0
Comprehensive QC of CPTAC3 sequence data
Automatic FASTQ to BAM pipeline (regular WES/WGS, 10x WES/WGS)
Obtain submitted reads and clinical info associated with CPTAC3 cases
Scripts for managing Cromwell workflows
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
CWL tool for calling germline variants using GATK
Workflow for GermlineWrapper project
CWL implementation of filter which merges VCFs according to BED file

importGDC

0 0
Command line client for Genomic Data Commons data downloads
Automated download of CPTAC3 data from GDC
Download CPTAC3 Batch 1 data on MGI and DC2
CWL project for VCF merge and filter tool
CWL project with Pindel germline calling and filtering

queryGDC

0 0
Command line client for Genomic Data Commons graphGL queries
Flag all SNP variants within a given distance of an indel
Driver scripts for CPTAC3 Batch 1 SomaticWrapper analyses
Simple workflow implementation for SomaticWrapper on MGI and standard Docker environments
Scripts for submission of CPTAC3 data

Toolkit

0 0
CWL implementation of Varscan Germline Caller
Modify fields of Varscan VCF files. CWL implementation

WUDocker

0 1
Utilities for launching docker in various Washington University environments