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Li Ding's Lab (@ding-lab)

ding-lab

Stars
595
Global Org. Rank 21,497 (Top 7 %)
Registered almost 12 years ago
Most used languages

Shell
24.6 %

Perl
21.5 %

R
18.5 %

Python
12.3 %

C++
6.2 %

Jupyter Notebook
4.6 %

Common Workflow Language 4.6 %

C
3.1 %

RMarkdown 1.5 %

PHP
1.5 %

JavaScript
1.5 %
Location 🇺🇸 United States
Country Total Rank 13,040
Country Ranking

RMarkdown 4

Common Workflow Language 12

Perl
134

R
567

C++
2,057

Shell
2,161

PHP
4,465

Jupyter Notebook
6,145

Python
7,994

msisensor

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

CharGer

Characterization of Germline variants

MuSiC2

identifying mutational significance in cancer genomes

hotspot3d

3D hotspot mutation proximity analysis tool

PanCanAtlasGermline

GenomeVIP

BreakPointSurveyor

A comprehensive pipeline to analyze and visualize structural variants

somaticwrapper

Detect somatic variants from tumor and normal WGS/WXS data

PanCan_snATAC_publication

Jupyter Notebook

BICSEQ2

BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA

VariantQC

Variant quality checking scripts.

cnvkit_pipeline

call copy number from WES(WXS)

misplice

Discover Mutation Induced Splice Sites

neoscan

predict neoantigen for indel and snvs

VirusScan

VirusScan Pipeline

cptac_methylation

Methylation array analysis pipeline for CPTAC

TinDaisy

CWL somatic variant caller

Common Workflow Language

gatk4wxscnv

Pipeline for WXS CNV using GATK4

germline_variant_snakemake

Snakemake workflow to call germline variant

ccRCC_snRNA_analysis

bassovac

Improved Bayesian inversion somatic caller

fuscia

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

griffin-fusion

Suite of fusion gene analysis tools

CPTAC3-RNA-related-pipeline

Gene/transcript expression; Fusion; de novo assembly

mc3_icgc_variant_pipeline

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

germlinewrapper

detect germline variants from normal samples

birdseed2vcf

Convert birdseed variant file with genotypes to a VCF file

cmds

Cohort DNA Copy Number Analysis

TinJasmine

CWL germline variant caller

Common Workflow Language

MIRMMR

Microsatellite Instability Regression using Methylation and Mutations in R

HotPho_Analysis

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

SomaticSV

CWL wrapper for Manta 1.4.0 and simple filter

CPTAC_miRNA

miRNA sequencing analysis for CPTAC

FASTQtoBAM

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

parse-kegg

Script to format KEGG pathway data for PathScan

infer_cnv_postprocesssing

pindel2

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

varscan_vcf_remap

Modify fields of Varscan VCF files. CWL implementation

pollock

A tool that classifies cells based on their gene expression

ancestry

Ancestry prediction from .bam files

Jupyter Notebook

10Xmapping

mapping somatic variants to cell barcodes in scRNA-Seq data

importGDC

Automated download of CPTAC3 data from GDC

calc-roi-covg

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.

gdc_qc_analysis

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

hotspot3d_portal

VEP_Filter

TinDaisy modules for filtering VCF based on VEP annotation

PDX-PanCanAtlas

Jupyter Notebook

rareprob2

Identifying significantly deleterious variants from germline variation and somatic mutational events

TinDaisy-Core

Core somatic caller scripts based on SomaticWrapper CWL branch

Fusion_hg38

SalmonTE

Pindel2BAM

Convert Pindel data into SAM & BAM formats.

phosphoproteomics

Directory hosting scripts used for phosphoproteomics analysis.

PDXToolkit

cptac_rna_expression

CPTAC RNA expression pipeline

druggability_databases

GATK_GermlineCaller

CWL tool for calling germline variants using GATK

VEP_annotate

CWL wrapper for VEP annotation

Common Workflow Language

LR-PKD

Analysis pipeline for haplotype-based variant detection

GDC.case.discover

Obtain submitted reads and clinical info associated with CPTAC3 cases

phospho-signaling

squaredancer

SV Detection for soft-clipped genomic or cDNA reads

CPTAC3_QC

Comprehensive QC of CPTAC3 sequence data

VirusIntegrate

Detect Virus integration site

CromwellRunner

Scripts for managing Cromwell workflows

HTAN_BRCA_publication

SomaticHaplotype

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