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cmds

 3  2
Cohort DNA Copy Number Analysis

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

calc-roi-covg

 2  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.

rareprob2

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

msisensor

 123  55
microsatellite instability detection using tumor only or paired tumor-normal data

bassovac

 5  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

 6  3
CWL somatic variant caller

TinJasmine

 3  0
CWL germline variant caller

VEP_annotate

 1  0
CWL wrapper for VEP annotation

pecgs-pipeline

 0  1
Dockerfile

dockers

 0  2
HTML

HTAN_bulkRNA_expression

 0  3
pipeline for HTAN bulk RNA-Seq data quantification
JavaScript

hotspot3d_portal

 2  3
Jupyter Notebook

PanCan_snATAC_publication

 12  4

ancestry

 2  0
Ancestry prediction from .bam files

PDX-PanCanAtlas

 2  2

mushroom

 1  0
A computational tool for identification of 3D multi-modal spatial neighborhoods

cptac-driver

 0  1
PHP

GenomeVIP

 20  5
Perl

MuSiC2

 59  20
identifying mutational significance in cancer genomes

hotspot3d

 45  26
3D hotspot mutation proximity analysis tool

somaticwrapper

 14  5
Detect somatic variants from tumor and normal WGS/WXS data

VirusScan

 9  7
VirusScan Pipeline

misplice

 8  5
Discover Mutation Induced Splice Sites

neoscan

 8  2
predict neoantigen for indel and snvs

10Xmapping

 4  2
mapping somatic variants to cell barcodes in scRNA-Seq data

germlinewrapper

 4  3
detect germline variants from normal samples

parse-kegg

 2  6
Script to format KEGG pathway data for PathScan

LR-PKD

 1  0
Analysis pipeline for haplotype-based variant detection

PepScan

 1  0
Detect variants from mass spectra data

squaredancer

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

TinDaisy-Core

 1  1
Core somatic caller scripts based on SomaticWrapper CWL branch

VirusIntegrate

 1  0
Detect Virus integration site

misplice_gcloud

 0  1

parse-cosmic

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

vcf2maf

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

CharGer

 95  37
Characterization of Germline variants

germline_variant_snakemake

 5  0
Snakemake workflow to call germline variant

fuscia

 4  6
Detection of chimeric transcripts (aka fusions) from barcoded single cell RNA-seq

birdseed2vcf

 3  7
Convert birdseed variant file with genotypes to a VCF file

cptac_rna_expression

 2  0
CPTAC RNA expression pipeline

infer_cnv_postprocesssing

 2  0

pollock

 2  2
A tool that classifies cells based on their gene expression

druggability_databases

 1  0

BioMine

 0  3
Bioinformatics data-mining

CPTAC3_splicing

 0  1
CPTAC3 RNA-seq splicing pipeline

SeqQEst

 0  1
Do quality control for BAMs
R

PanCanAtlasGermline

 42  14

cptac_methylation

 7  5
Methylation array analysis pipeline for CPTAC

ccRCC_snRNA_analysis

 6  5

gatk4wxscnv

 5  1
Pipeline for WXS CNV using GATK4

griffin-fusion

 5  3
Suite of fusion gene analysis tools

mc3_icgc_variant_pipeline

 4  2
Variant analysis pipeline to compare the public PCAWG and MC3 mutation files generated by ICGC and TCGA

HotPho_Analysis

 3  2
HotPho, a bioinformatics tool to discover spatially interacting phosphorylation sites and mutations in cancer

MIRMMR

 3  5
Microsatellite Instability Regression using Methylation and Mutations in R

ccRCC_sn_publication

 2  2
This github repository contains the data files and analysis code used in "Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma"

phosphoproteomics

 2  0
Directory hosting scripts used for phosphoproteomics analysis.

HTAN_BRCA_publication

 1  2

phospho-signaling

 1  0

SomaticHaplotype

 1  0
Object-oriented tools for phase block analysis and somatic mutation phasing using linked-read WGS

outlier

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

ST_subclone_publication

 0  1
Code for spatial subclone paper
RMarkdown

gdc_qc_analysis

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

BreakPointSurveyor

 19  3
A comprehensive pipeline to analyze and visualize structural variants

BICSEQ2

 15  4
BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA

VariantQC

 11  7
Variant quality checking scripts.

cnvkit_pipeline

 9  2
call copy number from WES(WXS)

CPTAC3-RNA-related-pipeline

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

CPTAC_miRNA

 3  3
miRNA sequencing analysis for CPTAC

FASTQtoBAM

 3  0
Automatic FASTQ to BAM pipeline (regular WES/WGS, 10x WES/WGS)

SomaticSV

 3  1
CWL wrapper for Manta 1.4.0 and simple filter

importGDC

 2  0
Automated download of CPTAC3 data from GDC

varscan_vcf_remap

 2  0
Modify fields of Varscan VCF files. CWL implementation

VEP_Filter

 2  0
TinDaisy modules for filtering VCF based on VEP annotation

CPTAC3_QC

 1  0
Comprehensive QC of CPTAC3 sequence data

CromwellRunner

 1  0
Scripts for managing Cromwell workflows

Fusion_hg38

 1  0

GATK_GermlineCaller

 1  0
CWL tool for calling germline variants using GATK

GDC.case.discover

 1  2
Obtain submitted reads and clinical info associated with CPTAC3 cases

PDXToolkit

 1  1

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