cancer-genomics
There are 26 repositories under cancer-genomics topic.
crazyhottommy / getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
Language:Shell 1140cBioPortal / cbioportal
cBioPortal for Cancer Genomics
Language:Java 597- maftools
PoisonAlien / maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
Language:R 435 dellytools / delly
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Language:C++ 422- pyGeno
tariqdaouda / pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Language:Python 309 seandavi / awesome-cancer-variant-databases
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
- Language:JavaScript 286
brentp / somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Language:Nim 259- Language:R 250
bioinform / somaticseq
An ensemble approach to accurately detect somatic mutations using SomaticSeq
Language:Python 190joiningdata / lollipops
Lollipop-style mutation diagrams for annotating genetic variations.
Language:Go 180genome-spy / genome-spy
A visualization grammar and GPU-accelerated toolkit for genomic data
Language:JavaScript 172greenelab / tybalt
Training and evaluating a variational autoencoder for pan-cancer gene expression data
Language:HTML 162kharchenkolab / numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
Language:R 161- Language:C 153
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.
Language:Python 149ding-lab / msisensor
microsatellite instability detection using tumor only or paired tumor-normal data
Language:C++ 124broadinstitute / depmap_omics
What you need to process the Quarterly DepMap-Omics releases from Terra
Language:HTML 105- Language:TypeScript 100
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.
Language:Python 97GooglingTheCancerGenome / sv-callers
Snakemake-based workflow for detecting structural variants in genomic data
Language:Python 73FunGeST / Palimpsest
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
Language:R 68caravagnalab / revolver
REVOLVER - Repeated Evolution in Cancer
Language:R 64- Language:Perl 59
- Language:Python 59
iVis-at-Bilkent / pathway-mapper
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Language:TypeScript 55rhshah / IMPACT-Pipeline
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
Language:Perl 55- Language:R 55
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.
Language:Python 53lynnlangit / TeamTeri
Bioinformatics on GCP, AWS or Azure
Language:Shell 53griffithlab / civic-client
Web client for CIViC: Clinical Interpretations of Variants in Cancer
Language:JavaScript 50getzlab / deTiN
DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
Language:Jupyter Notebook 49BIMSBbioinfo / maui
Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
Language:Jupyter Notebook 48SigProfilerPlotting 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.
Language:Python 45Identifying tumor cells at the single-cell level using machine learning
Language:HTML 43- Language:Java 39
