Li Ding's Lab dinglab.wustl.edu lding@wustl.eduLi Ding's Lab at the Washington University School of Medicine 84 0 137 699 336 No Language 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 1 1 Identifying significantly deleterious variants from germline variation and somatic mutational eventsC++ msisensor 129 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 2 Dockerfile dockers 0 2 HTML HTAN_bulkRNA_expression 0 4 pipeline for HTAN bulk RNA-Seq data quantificationJavaScript hotspot3d_portal 2 3 Jupyter Notebook PanCan_snATAC_publication 17 4 mushroom 11 1 A computational tool for identification of 3D multi-modal spatial neighborhoods ancestry 4 1 Ancestry prediction from .bam files PDX-PanCanAtlas 3 3 cptac-driver 0 1 PHP GenomeVIP 20 5 Perl MuSiC2 61 20 identifying mutational significance in cancer genomes hotspot3d 47 26 3D hotspot mutation proximity analysis tool somaticwrapper 15 9 Detect somatic variants from tumor and normal WGS/WXS data VirusScan 11 7 VirusScan Pipeline misplice 9 5 Discover Mutation Induced Splice Sites 10Xmapping 8 2 mapping somatic variants to cell barcodes in scRNA-Seq data neoscan 8 2 predict neoantigen for indel and snvs germlinewrapper 4 3 detect germline variants from normal samples parse-kegg 2 6 Script to format KEGG pathway data for PathScan COCOONS 1 0 COrrecting CO-Occuring multi-Nucleotide variation 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 isoformsPython CharGer 98 37 Characterization of Germline variants fuscia 6 6 Detection of chimeric transcripts (aka fusions) from barcoded single cell RNA-seq germline_variant_snakemake 5 0 Snakemake workflow to call germline variant morph 5 0 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 3 A tool that classifies cells based on their gene expression druggability_databases 1 0 SeqQEst 1 2 Do quality control for BAMs BioMine 0 3 Bioinformatics data-mining CPTAC3_splicing 0 1 CPTAC3 RNA-seq splicing pipeline R PanCanAtlasGermline 44 14 ST_subclone_publication 10 4 Code for spatial subclone paper ccRCC_snRNA_analysis 8 5 cptac_methylation 8 5 Methylation array analysis pipeline for CPTAC gatk4wxscnv 5 1 Pipeline for WXS CNV using GATK4 griffin-fusion 5 3 Suite of fusion gene analysis tools ccRCC_sn_publication 4 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" 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 HTAN_BRCA_publication 3 2 MIRMMR 3 5 Microsatellite Instability Regression using Methylation and Mutations in R phosphoproteomics 3 0 Directory hosting scripts used for phosphoproteomics analysis. Intratumor_heterogeneity 1 0 phospho-signaling 1 0 SomaticHaplotype 1 0 Object-oriented tools for phase block analysis and somatic mutation phasing using linked-read WGS spatial_driver_co-detection_paper 1 1 Code for spatial driver co-detection paper ffpefiltering 0 1 Use MicroSec for FFPE filtering 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 MC3Shell BreakPointSurveyor 20 3 A comprehensive pipeline to analyze and visualize structural variants BICSEQ2 16 5 BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA VariantQC 11 7 Variant quality checking scripts. cnvkit_pipeline 10 4 call copy number from WES(WXS) CPTAC3-RNA-related-pipeline 5 3 Gene/transcript expression; Fusion; de novo assembly CPTAC_miRNA 4 2 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 PDXToolkit 2 1 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 queryGDC 1 0 Command line client for Genomic Data Commons graphGL queries GATK4SCNA 0 2 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
