41 Open Source Cancer Genomics Software Projects
Free and open source cancer genomics code projects including engines, APIs, generators, and tools.
Getting Started With Genomics Tools And Resources 495 ⭐
Unix, R and python tools for genomics and data science
Awesome Cancer Variant Databases 192 ⭐
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
Somalier 115 ⭐
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Palimpsest 54 ⭐
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
Impact Pipeline 46 ⭐
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
Detin 38 ⭐
DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
Sigprofilerextractor 45 ⭐
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.
Sigprofilermatrixgenerator 39 ⭐
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.
Maui 26 ⭐
Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
Clonealign 24 ⭐
Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data
Wittelab Orchid 24 ⭐
A novel management, annotation, and machine learning framework for analyzing cancer mutations
Sigprofilerplotting 22 ⭐
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.
Variants2neoantigen 20 ⭐
A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
Cancerdiscover 17 ⭐
Open-source software pipeline for cancer classification from high-throughput data using machine learning.
Sigven Cacao 17 ⭐
Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
Neural Ensemble Method For Cancer Prediction 13 ⭐
A Snapshot Neural Ensemble Method for Cancer Type Prediction Based on Copy Number Variations