Most popular bioinformatics repositories and open source projects

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.

13   63   63  

apbs

Software for biomolecular electrostatics and solvation calculations

15   63   63  

NeuroSEED

Implementation of Neural Distance Embeddings for Biological Sequences...

17   63   63  

preseq

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

12   63   63  

tutorial

Tutorials on machine learning, artificial intelligence, data science w...

6   63   63  

EBImage

:art: Image processing toolbox for R

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DeepChrome

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

14   62   62  

pymsfilereader

Thermo MSFileReader Python bindings

24   62   62  

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...

23   62   62  

rosalind-solutions

my solutions to problems from Rosalind.

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ProtFlash

ProtFlash: A lightweight protein language model

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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

19   61   61  

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...

12   61   61  

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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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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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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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

17   58   58  

arpeggio

Calculation of interatomic interactions in molecular structures

23   58   58  

sirius

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

15   58   58  

FlashFry

FlashFry: The rapid CRISPR target site characterization tool

10   58   58  

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...

19   57   57  

telomeric-identifier

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

4   57   57  

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...

5   55   55  

taxprofiler

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

20   55   55  

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

7   54   54  

biscuit

BISulfite-seq CUI Toolkit

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Toolkit

The MPI Bioinformatics Toolkit

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OmicLearn

🧪 🖥 Transparent exploration of machine learning for biomarker discov...

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chip-atlas

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

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