Pinned Repositories
annotatr
Annotation of Genomic Regions to Genomic Annotations
DDCV
A Visualized Shiny App to Evaluate Drug-Drug Interaction
EAGLE_LUAD
Genetic and Epigenetic Intratumor Heterogeneity Impacts Prognosis of Lung Adenocarcinoma
mSigPortal
Integrative mutational signature portal (MsigPortal) for cancer genomic study
Sherlock-Lung
Bioinformatic analysis scripts for Sherlock-Lung project
SigProfilerMatrixGenerator
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
SigProfilerPlotting
SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.
SigProfilerPlottingR
An R wrapper for running the SigProfilerPlotting framework
xtmgah's Repositories
xtmgah/HiC_tools
A collection of tools for Hi-C data analysis
xtmgah/SigProfilerMatrixGenerator
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
xtmgah/ACAT
xtmgah/Alleloscope
Alleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separately or in combination). Allele-specific estimation allows for the more accurate delineation of copy number states and the detection of subclonal copy-neutral loss-of-heterozygosity and mirrored CNA events. On scATAC-seq data, Alleloscope allows integrative multi-omic analysis of allele-specific copy number and chromatin accessibility for the same cell.
xtmgah/arriba
Fast and accurate gene fusion detection from RNA-Seq data
xtmgah/autoReg
R package autoReg
xtmgah/awesome-multi-omics
List of software packages for multi-omics analysis
xtmgah/bamsnap
xtmgah/CHM13
The complete sequence of a human genome
xtmgah/circdna
Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
xtmgah/CleanCNA
An R package to classify a copy number call as of high or low quality, to re-estimate purity and ploidy parameters based on a set of collected metrics, and to iteratively rerun the copy number calling process to provide a high quality set of copy number calls using WGS data.
xtmgah/correlation
:link: Methods for Correlation Analysis
xtmgah/cuplr
Predicting tumor type using WGS derived features
xtmgah/Data-Viz-ggplot2
Data Visualization for Environmental Epidemiology with ggplot2: Mastering Presentation-Grade Figures
xtmgah/DCEG-workshops.github.io
NCI DCEG workshops
xtmgah/dunnr
My personal R package
xtmgah/easystats
:milky_way: The R easystats-project
xtmgah/esquisse
RStudio add-in to make plots interactively with ggplot2
xtmgah/FaNDOM
Fast Nested Distance aligner for Optical Maps
xtmgah/FASTK
A fast K-mer counter for high-fidelity shotgun datasets
xtmgah/fivex
Interactive eQTL visualizations
xtmgah/GEMSCAN
Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.
xtmgah/GNOSIS
GNOSIS was developed to enable the exploration, visualisation and analysis of clinical and CNA summary data obtained from cBioPortal, in this case the METABRIC data.
xtmgah/HLA-TAPAS
HLA-TAPAS pipeline for HLA association and fine-mapping studies
xtmgah/RepairSig
xtmgah/RF-mut-f
A random forest implementation to filter germline mutations of tumor-only samples
xtmgah/ShinyCell
Shiny Interactive Web Apps for Single-Cell Data
xtmgah/skidb
Reference data utilities for mskilab
xtmgah/somaticfreq
knowledge-based genotyping of cancer hotspots from the tumor BAM files
xtmgah/SVAFotate