cancer-genomics
There are 291 repositories under cancer-genomics topic.
crazyhottommy/getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
cBioPortal/cbioportal
cBioPortal for Cancer Genomics
PoisonAlien/maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
dellytools/delly
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
tariqdaouda/pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
seandavi/awesome-cancer-variant-databases
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
eweitz/ideogram
Chromosome visualization for the web
brentp/somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
sigven/pcgr
Personal Cancer Genome Reporter (PCGR)
bioinform/somaticseq
An ensemble approach to accurately detect somatic mutations using SomaticSeq
joiningdata/lollipops
Lollipop-style mutation diagrams for annotating genetic variations.
genome-spy/genome-spy
A visualization grammar and GPU-accelerated toolkit for genomic data
kharchenkolab/numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
greenelab/tybalt
Training and evaluating a variational autoencoder for pan-cancer gene expression data
AlexandrovLab/SigProfilerExtractor
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
nygenome/lancet
Microassembly based somatic variant caller for NGS data
ding-lab/msisensor
microsatellite instability detection using tumor only or paired tumor-normal data
broadinstitute/depmap_omics
What you need to process the Quarterly DepMap-Omics releases from Terra
cBioPortal/cbioportal-frontend
React Frontend of cBioPortal :tada:
AlexandrovLab/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.
GooglingTheCancerGenome/sv-callers
Snakemake-based workflow for detecting structural variants in genomic data
FunGeST/Palimpsest
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
caravagnalab/revolver
REVOLVER - Repeated Evolution in Cancer
AmpliconSuite/AmpliconSuite-pipeline
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
ding-lab/MuSiC2
identifying mutational significance in cancer genomes
murphycj/AGFusion
Python package to annotate and visualize gene fusions.
sigven/cpsr
Cancer Predisposition Sequencing Reporter (CPSR)
iVis-at-Bilkent/pathway-mapper
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
rhshah/IMPACT-Pipeline
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
lynnlangit/TeamTeri
Bioinformatics on GCP, AWS or Azure
griffithlab/civic-client
Web client for CIViC: Clinical Interpretations of Variants in Cancer
BIMSBbioinfo/maui
Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
getzlab/deTiN
DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
AlexandrovLab/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.
BIMSBbioinfo/ikarus
Identifying tumor cells at the single-cell level using machine learning
genome-nexus/genome-nexus
Backend server for Genome Nexus