bioinformatics
Repositories (1438)
Benchmarking programming languages/implementations for common tasks in Bioinformatics
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
C-library for calculating Solvent Accessible Surface Areas
R inside Python
Bioinformatics Project. Trying to find out the most influential metabolomic biomarkers(from 158) for predicting Lung Cancer. Also, trying to make some...
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of oper...
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
Helper Functions for Interactive Tree Of Life (iTOL)
🌿: ABM & GIS for philological, archaeological, and anthropological data.
Py3plex - A multilayer complex network visualization and analysis library in python3
Population-scale Ancestral Recombination Graph (ARG) library
R package for analyzing single-cell RNA-seq data
A (mostly) universal methylation extractor for BS-seq experiments.
The sources of the openSNP website
Fast, efficient RNA-Seq metrics for quality control and process optimization
Fast multi-line FASTA/Q reader in several programming languages
Precision genomics for everyone, everywhere. Powered by private AI.
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...
tools for analyzing and exploring genetic relationships
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
Code examples of fast and simple k-mer counters for tutorial purposes
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
Genomics Extension for SQLite
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works e...
MrBiomics: Composable modules and recipes automate bioinformatics for multi-omics analyses
genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with advanced fil...
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
Similarity networks of biosynthetic gene clusters
sensitive and precise assembly of short sequencing reads
Yet another k-mer analyzer
The Pharmacogenomic Clinical Annotation Tool
Version 5 of the CAFE phylogenetics software
A simple Snakemake profile for Slurm without --cluster-config
Identify and find telomeres, or telomeric repeats in a genome.
WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
SGAS: Sequential Greedy Architecture Search (CVPR'2020) https://www.deepgcns.org/auto/sgas
Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
RiboNucleic Acid (RNA) Language Model
Biological sequences for the julia language
🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiang...
Cython bindings and Python interface to HMMER3.
A fast whole-genome aligner based on de Bruijn graphs
Open source biolab
SemiBin: metagenomics binning with self-supervised deep learning