425 Open source projects that are alternatives of or similar to Awesome Cancer Variant Databases

An R package for reproducible and automated ADMIXTOOLS analyses

A robust model for quantitative comparison of ChIP-Seq data sets.

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

FastQC port to Qt5: A quality control tool for high throughput sequence data.

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Data intensive science for everyone.

GRAph-based Finding of Individual Motif Occurrences

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Aggregate results from bioinformatics analyses across many samples into a single report.

The BridgeDb Library source code

Bioinformatics library for .NET

A plotly.js React component from Plotly 📈

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

code for reading and processing Allen Institute for Brain Science data

Toolkit for preparing genomes for submission to NCBI

Python and C++ code for reading and writing genomics data.

Computational Analysis of Novel Drug Opportunities

A robust and fast clustering method for amplicon-based studies

The Ensembl Compara Perl API and SQL schema

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

Bayesian haplotype-based mutation calling

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

Backend server for Genome Nexus

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

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.

C library for high-throughput sequencing data formats

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.

Annotated data.

Single-cell copy number calling and event history reconstruction.

Biostar Q&A

A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

Haplotype VCF comparison tools

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

A curated list of Cheminformatics libraries and software.

A comprehensive library for computational molecular biology

Official git repository for Biopython (originally converted from CVS)

Versatile open-source tool for microbiome analysis

cython + htslib == fast VCF and BCF processing

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

Workflow Description Language - Specification and Implementations

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

Protein Graph Library

Remote protein homology detection suite.

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

An ultrafast memory-efficient short read aligner

Structural variant toolkit for VCFs

A cross-platform command-line tool for executing jobs in parallel

Proof-of-concept seq-to-graph mapper and graph generator

Intuitive local web frontend for the BLAST bioinformatics tool

RAxML Next Generation: faster, easier-to-use and more flexible

Python for Bioinformatics

The sources of the openSNP website

A tool to circularize genome assemblies

Genome inference from a population reference graph

The uncompromising Snakemake code formatter