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cmds

 3  2
Cohort DNA Copy Number Analysis

GDAN.catalog

 1  0

SalmonTE

 1  0

breakdancer

 0  2
SV detection from paired end reads mapping

PASSion

 0  1
Paired-end RNA-Seq splice site detection

publicDEPO

 0  2
Public page for users to ask questions, make comments, or file bug issues.
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

 108  49
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

Pindel2BAM

 1  4
Convert Pindel data into SAM & BAM formats.

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.
Common Workflow Language

TinDaisy

 4  1
CWL somatic variant caller
Dockerfile

dockers

 0  2
JavaScript

hotspot3d_portal

 2  3
Jupyter Notebook

ancestry

 2  0
Ancestry prediction from .bam files

PDX-PanCanAtlas

 1  1
PHP

GenomeVIP

 16  5
Perl

MuSiC2

 52  22
identifying mutational significance in cancer genomes

hotspot3d

 40  24
3D hotspot mutation proximity analysis tool

somaticwrapper

 7  2
Detect somatic variants from tumor and normal WGS/WXS data

misplice

 6  5
Discover Mutation Induced Splice Sites

neoscan

 6  1
predict neoantigen for indel and snvs

VirusScan

 5  6
VirusScan Pipeline

parse-kegg

 2  6
Script to format KEGG pathway data for PathScan

germlinewrapper

 1  2
detect germline variants from normal samples

LR-PKD

 1  0
Analysis pipeline for haplotype-based variant detection

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

misplice_gcloud

 0  1

parse-cosmic

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

TinDaisy-Core

 0  1
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

 72  34
Characterization of Germline variants

germline_variant_snakemake

 5  0
Snakemake workflow to call germline variant

birdseed2vcf

 2  6
Convert birdseed variant file with genotypes to a VCF file

cptac_rna_expression

 1  0
CPTAC RNA expression pipeline

fuscia

 1  4
Detection of chimeric transcripts (aka fusions) from barcoded single cell RNA-seq

pollock

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

BioMine

 0  2
Bioinformatics data-mining

CPTAC3_splicing

 0  1
CPTAC3 RNA-seq splicing pipeline

SeqQEst

 0  1
Do quality control for BAMs
R

PanCanAtlasGermline

 32  14

cptac_methylation

 5  3
Methylation array analysis pipeline for CPTAC

gatk4wxscnv

 5  1
Pipeline for WXS CNV using GATK4

griffin-fusion

 4  2
Suite of fusion gene analysis tools

MIRMMR

 3  4
Microsatellite Instability Regression using Methylation and Mutations in R

mc3_icgc_variant_pipeline

 2  2
Variant analysis pipeline to compare the public PCAWG and MC3 mutation files generated by ICGC and TCGA

HotPho_Analysis

 1  2
HotPho, a bioinformatics tool to discover spatially interacting phosphorylation sites and mutations in cancer

phosphoproteomics

 1  0
Directory hosting scripts used for phosphoproteomics analysis.

phospho-signaling

 1  0

ccRCC_snRNA_analysis

 0  3

outlier

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

 6  6
Variant quality checking scripts.

BICSEQ2

 5  2
BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA

CPTAC3-RNA-related-pipeline

 4  3
Gene/transcript expression; Fusion; de novo assembly

cnvkit_pipeline

 3  2
call copy number from WES(WXS)

CPTAC3.catalog

 3  1
Details about CPTAC3 data at GDC and in Ding Lab

SomaticSV

 3  1
CWL wrapper for Manta 1.4.0 and simple filter

CPTAC_miRNA

 2  1
miRNA sequencing analysis for CPTAC

FASTQtoBAM

 2  0
Automatic FASTQ to BAM pipeline (regular WES/WGS, 10x WES/WGS)

VEP_Filter

 2  0
TinDaisy modules for filtering VCF based on VEP annotation

CPTAC3_QC

 1  0
Comprehensive QC of CPTAC3 sequence data

importGDC.CPTAC3

 1  0
Automated download of CPTAC3 data from GDC

PDXToolkit

 1  1

varscan_vcf_remap

 1  0
Modify fields of Varscan VCF files. CWL implementation

CPTAC3.case.discover

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

GATK4SCNA

 0  1

Pindel_GermlineCaller

 0  1
CWL project with Pindel germline calling and filtering

RegulatoryGermline

 0  1

submit.CPTAC3

 0  1
Scripts for submission of CPTAC3 data

WUDocker

 0  2
Utilities for launching docker in various Washington University environments