Pinned Repositories
ACE
Absolute Copy Number Estimation using low-coverage whole genome sequencing data
BLADE
BLADE: Bayesian Log-normAl DEconvolution for enhanced in silico microdissection of bulk gene expression data
ddPCR
falco
Amplicon variant caller
OncoBLADE
Hidden RNA profiles of cells in the tumor microenvironment accurately revealed by malignant cell fraction-informed deconvolution
QDNAseq.dev
QDNAseq.hg19
QDNAseq.mm10
QDNAseq.snakemake
WES-snake
snakemake from fastq to annotated mutation calling using MUTECT2
Tumor Genome Analysis Core's Repositories
tgac-vumc/BLADE
BLADE: Bayesian Log-normAl DEconvolution for enhanced in silico microdissection of bulk gene expression data
tgac-vumc/ACE
Absolute Copy Number Estimation using low-coverage whole genome sequencing data
tgac-vumc/OncoBLADE
Hidden RNA profiles of cells in the tumor microenvironment accurately revealed by malignant cell fraction-informed deconvolution
tgac-vumc/WES-snake
snakemake from fastq to annotated mutation calling using MUTECT2
tgac-vumc/ddPCR
tgac-vumc/falco
Amplicon variant caller
tgac-vumc/QDNAseq.dev
tgac-vumc/QDNAseq.snakemake
tgac-vumc/QDNAseq.hg19
tgac-vumc/QDNAseq.mm10
tgac-vumc/RNA-seq
RNA-seq analysis pipeline based on Snakemake
tgac-vumc/small_scripts
small things to be shared with others.
tgac-vumc/translocation-snake
Translocation detection pipeline by next generation sequencing. A combined approach of BreaKmer, Gridss, Wham and novoBreak.
tgac-vumc/CGHbase
tgac-vumc/CGHcall
tgac-vumc/CNA_clonality
Code associated with manuscript "Diagnostic test accuracy to determine clonality between multiple tumors with pulmonary involvement using genome-wide copy number analysis"
tgac-vumc/CopywritR-snake
Estimate copy number read counts from whole-exome sequencing data using CopyWritR
tgac-vumc/lgg-snakemake
Snakemake pipeline for analysis of methylation data of long and short survivors of 1p/19q-codeleted oligodendroglioma
tgac-vumc/spatstat_vectra
Marked point process modeling of Vectra data
tgac-vumc/TCGA_purity
tgac-vumc/tumor-only-snakemake
tgac-vumc/WECCA
Weighted hierarchical clustering of array CGH data using (call probabilities)