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10xmapping

mapping somatic variants to cell barcodes in scRNA-Seq data

3d-portal

3D proximity visulization portal

ancestry

Ancestry prediction from .bam files

ancestry-pipeline

Ding lab ancestry pipeline

ase_analysis

bassovac

Improved Bayesian inversion somatic caller

bassovacmate

a wrapper for Bassovac tool

bicseq2

BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA

biomine

Bioinformatics data-mining

birdseed2vcf

Convert birdseed variant file with genotypes to a VCF file

breakdancer

SV detection from paired end reads mapping

breakpointsurveyor

A comprehensive pipeline to analyze and visualize structural variants

breakpointsurveyor-core

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.

catalog3.gtac

Create catalog files for sequence data generated by GTAC@MGI

ccrcc_drug.catalog

ccrcc_sn_publication

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"

ccrcc_snrna_analysis

charger

Characterization of Germline variants

clinvar

This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.

cmds

Cohort DNA Copy Number Analysis

cnvkit_pipeline

call copy number from WES(WXS)

cocoons

COrrecting CO-Occuring multi-Nucleotide variation

cptac-driver

cptac3-rna-related-pipeline

Gene/transcript expression; Fusion; de novo assembly

cptac3.missinganalysis

Ad hoc scripts to identify analyses needing to be performed for CPTAC3 contract work

cptac3_qc

Comprehensive QC of CPTAC3 sequence data

cptac3_splicing

CPTAC3 RNA-seq splicing pipeline

cptac_methylation

Methylation array analysis pipeline for CPTAC

cptac_mirna

miRNA sequencing analysis for CPTAC