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The Top 23 Bioinformatics Cancer Genomics Open Source Projects

Open source projects categorized as Bioinformatics Cancer Genomics
Categories > Data Processing > Bioinformatics
Categories > Science > Cancer Genomics
Getting Started With Genomics Tools And Resources ⭐ 991
Unix, R and python tools for genomics and data science
most recent commit 3 months ago
Maftools ⭐ 400
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
most recent commit 3 months ago
Awesome Cancer Variant Databases ⭐ 284
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
most recent commit 6 months ago
Pygeno ⭐ 242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
total releases 18most recent commit 4 years ago
Somalier ⭐ 224
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
most recent commit 7 months ago
Genome Spy ⭐ 150
A visualization grammar and GPU-accelerated toolkit for genomic data
dependent packages 3total releases 41most recent commit 3 months agonpm @genome-spy/core} Downloads
Sigprofilerextractor ⭐ 132
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.
dependent packages 3total releases 50most recent commit 5 months agopypi SigProfilerExtractor} Downloads
Msisensor ⭐ 99
microsatellite instability detection using tumor only or paired tumor-normal data
most recent commit 3 years ago
Sigprofilermatrixgenerator ⭐ 91
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.
dependent packages 10total releases 102most recent commit 3 months agopypi SigProfilerMatrixGenerator} Downloads
Palimpsest ⭐ 56
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
most recent commit 3 years ago
Pathway Mapper ⭐ 52
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
dependent packages 2total releases 15most recent commit a year agonpm pathway-mapper} Downloads
Sv Callers ⭐ 52
Snakemake-based workflow for detecting structural variants in genomic data
most recent commit a year ago
Teamteri ⭐ 50
Genomics (computational bioinformatic data analysis) running on GCP, AWS or Azure
most recent commit 8 months ago
Maui ⭐ 47
Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
total releases 17most recent commit 10 months ago
Agfusion ⭐ 46
Python package to annotate and visualize gene fusions.
dependent packages 1total releases 38most recent commit a year agopypi agfusion} Downloads
Sevenbridges Python ⭐ 44
SevenBridges Python Api bindings
dependent packages 3total releases 117most recent commit 3 months agopypi sevenbridges-python} Downloads
Ikarus ⭐ 34
Identifying tumor cells at the single-cell level using machine learning
most recent commit a year ago
Orchid ⭐ 29
A novel management, annotation, and machine learning framework for analyzing cancer mutations
most recent commit a year ago
Sevenbridges R ⭐ 27
Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R
most recent commit 3 years ago
Cfdnapro ⭐ 20
cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis
most recent commit 7 months ago
Sigprofilersimulator ⭐ 18
SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
most recent commit 7 months ago
Sigprofilermatrixgeneratorr ⭐ 17
R wrapper for utilizing the SigProfilerMatrixGenerator framework
most recent commit a year ago
Ngcgh ⭐ 17
Tools for producing pseudo-cgh of next-generation sequencing data
total releases 14most recent commit 8 years ago
The 7 Most Depended On Bioinformatics Cancer Genomics Open Source Projects
Genome Spy ⭐ 150
A visualization grammar and GPU-accelerated toolkit for genomic data
dependent packages 3total releases 41latest release November 24, 2023most recent commit 3 months agonpm @genome-spy/core} Downloads
Sevenbridges Python ⭐ 44
SevenBridges Python Api bindings
dependent packages 3total releases 117latest release November 02, 2022most recent commit 3 months agopypi sevenbridges-python} Downloads
Pathway Mapper ⭐ 52
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
dependent packages 2total releases 15latest release May 26, 2023most recent commit a year agonpm pathway-mapper} Downloads
Agfusion ⭐ 46
Python package to annotate and visualize gene fusions.
dependent packages 1total releases 38latest release February 10, 2023most recent commit a year agopypi agfusion} Downloads
The 10 Latest Releases In Bioinformatics Cancer Genomics Open Source Projects
Genome Spy ⭐ 150
A visualization grammar and GPU-accelerated toolkit for genomic data
dependent packages 3total releases 41latest release November 24, 2023most recent commit 3 months agonpm @genome-spy/core} Downloads
Pathway Mapper ⭐ 52
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
dependent packages 2total releases 15latest release May 26, 2023most recent commit a year agonpm pathway-mapper} Downloads
Agfusion ⭐ 46
Python package to annotate and visualize gene fusions.
dependent packages 1total releases 38latest release February 10, 2023most recent commit a year agopypi agfusion} Downloads
Sevenbridges Python ⭐ 44
SevenBridges Python Api bindings
dependent packages 3total releases 117latest release November 02, 2022most recent commit 3 months agopypi sevenbridges-python} Downloads
Pygeno ⭐ 242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
total releases 18latest release December 15, 2021most recent commit 4 years ago
Maui ⭐ 47
Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
total releases 17latest release April 09, 2021most recent commit 10 months ago
Ngcgh ⭐ 17
Tools for producing pseudo-cgh of next-generation sequencing data
total releases 14latest release December 18, 2013most recent commit 8 years ago
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