Most popular bioinformatics repositories and open source projects

singleCellHaystack

Finding surprising needles (=genes) in haystacks (=single cell transcr...

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obi

The Ontology for Biomedical Investigations

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OpenGene.jl

(No maintenance) OpenGene, core libraries for NGS data analysis and bi...

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catch

A package for designing compact and comprehensive capture probe sets.

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apbs

Software for biomolecular electrostatics and solvation calculations

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NeuroSEED

Implementation of Neural Distance Embeddings for Biological Sequences...

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preseq

Software for predicting library complexity and genome coverage in high...

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ProtFlash

ProtFlash: A lightweight protein language model

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DeepChrome

Bioinformatics16: DeepChrome: Deep-learning for predicting gene expre...

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pymsfilereader

Thermo MSFileReader Python bindings

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MIToS.jl

Mutual Information Tools for protein Sequence analysis in Julia

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sv-callers

Snakemake-based workflow for detecting structural variants in genomic...

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rosalind-solutions

my solutions to problems from Rosalind.

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gatb-core

Core library of the Genome Analysis Toolbox with de-Bruijn graph

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Fastaq

Python3 scripts to manipulate FASTA and FASTQ files

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Coursera-Bioinformatics

My solution to Bioinformatics Specialization (Finding Hidden Messages...

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coolpuppy

A versatile tool to perform pile-up analysis on Hi-C data in .cool for...

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GeneticsMakie.jl

🧬High-performance genetics-related data visualization using Makie.jl

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pangraph

A bioinformatic toolkit to align genome assemblies into pangenome grap...

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FluentDNA

FluentDNA allows you to browse sequence data of any size using a zoomi...

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pymod

PyMod 3 - sequence similarity searches, multiple sequence/structure al...

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simplesam

Simple pure Python SAM parser and objects for working with SAM records

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epa-ng

Massively parallel phylogenetic placement of genetic sequences

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EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline

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Packages

Aim to be the bioinformatics repository with more and newer packages

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FlashFry

FlashFry: The rapid CRISPR target site characterization tool

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mulled

Mulled - Automatized Containerized Software Repository

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GenomeGraphs.jl

A modern genomics framework for julia

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biolink-api

API for linked biological knowledge

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asap

A scalable bacterial genome assembly, annotation and analysis pipeline

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arpeggio

Calculation of interatomic interactions in molecular structures

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sirius

SIRIUS is a software for discovering a landscape of de-novo identifica...

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SV2

Support Vector Structural Variation Genotyper

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sns

Analysis pipelines for genomic sequencing data

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gblastn

G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the w...

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liblevenshtein-java

Various utilities regarding Levenshtein transducers. (Java)

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telomeric-identifier

Identify and find telomeres, or telomeric repeats in a genome.

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haddock3

The official repo of the new modular BioExcel2 version of HADDOCK

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pathogen-informatics-training

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BioAlignments.jl

Sequence alignment tools

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uta

Universal Transcript Archive: comprehensive genome-transcript alignmen...

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gfapy

Gfapy: a flexible and extensible software library for handling sequenc...

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taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun and long-read...

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chip-atlas

ChIP-Atlas: Browse and analyze all public ChIP/DNase-seq data on your...

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manyfold

🧬 ManyFold: An efficient and flexible library for training and valida...

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single-cell-training

SIB course on single cell transcriptomics by mostly using the Seurat p...

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raptor

Graph-based mapping of long sequences, noisy or HiFi.

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CfdnaPattern

Pattern Recognition for Cell-free DNA

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Arioc

Arioc: GPU-accelerated DNA short-read alignment

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paladin

Protein Alignment and Detection Interface

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