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

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

Genomics using open source tools, running on GCP or AWS

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 SigProfilerMatrixGen…

Unix, R and python tools for genomics and data science

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Snakemake-based workflow for detecting structural variants in WGS data

Next generation sequencing reads de novo assembler.

Genome assembly evaluation tool

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Ten Quick Tips for Deep Learning in Biology

Lollipop-style mutation diagrams for annotating genetic variations.

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

A curated list of bioinformatics bench-marking papers and resources.

Cuneiform distributed programming language

Python package for graph neural networks in chemistry and biology

Microassembly based somatic variant caller for NGS data

A genome browser that shows long reads and complex variants better

Curated (meta)list of resources for Biology.

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

A repository for setting up a RNAseq workflow

nim wrapper for htslib for parsing genomics data files

Simple simulation of single-cell RNA sequencing data

Bioconductor cheat sheet

Toolset for SV simulation, comparison and filtering

BioGrakn Knowledge Graph

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

Reads simulator

R package for analyzing single-cell RNA-seq data

A powerful open source data warehouse system

Package for fetching metadata and downloading data from SRA/ENA/GEO

Rapid large-scale prokaryote pan genome analysis

parallel fastq-dump wrapper

GenomeTools genome analysis system.

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

code for reading and processing Allen Institute for Brain Science data

Bayesian haplotype-based mutation calling

Annotated data.

A comprehensive library for computational molecular biology

Protein Graph Library

Fast multi-line FASTA/Q reader in several programming languages

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Chromosome visualization for the web

Personal Cancer Genome Reporter (PCGR)

Training and evaluating a variational autoencoder for pan-cancer gene expression data

Tools for working with genomic and high throughput sequencing data.

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Deep learning infrastructure for bioinformatics

Syntax highlighting for computational biology

ECG classification programs based on ML/DL methods

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results