Most popular bioinformatics repositories and open source projects

truvari

Structural variant toolkit for VCFs

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deep-rules

Ten Quick Tips for Deep Learning in Biology

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miniprot

Align proteins to genomes with splicing and frameshift

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bioinformatics-workflows

minimal example implementations for bioinformatics workflow managers

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bioinf-python

Python for Bioinformatics

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cuneiform

Cuneiform distributed programming language

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weekly

生信爱好者周刊（每周日发布）

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hgvs

Python library to parse, format, validate, normalize, and map sequence...

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Blacklist

Application for making ENCODE Blacklists

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pronto

A Python frontend to (Open Biomedical) Ontologies.

42   211   211  

somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "l...

31   204   204  

snp-sites

Finds SNP sites from a multi-FASTA alignment file

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masurca

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scgen

Single cell perturbation prediction

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goleft

goleft is a collection of bioinformatics tools distributed under MIT l...

24   201   201  

Artemis

Artemis is a free genome viewer and annotation tool that allows visual...

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bigsnpr

R package for the analysis of massive SNP arrays.

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AfterQC

Automatic Filtering, Trimming, Error Removing and Quality Control for...

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SOAPdenovo2

Next generation sequencing reads de novo assembler.

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pyfastx

a python package for fast random access to sequences from plain and gz...

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circlator

A tool to circularize genome assemblies

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drep

Rapid comparison and dereplication of genomes

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MrBayes

MrBayes is a program for Bayesian inference and model choice across a...

73   191   191  

tools

Python package with helper tools for the nf-core community.

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HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, nor...

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Workshop

课题组每周研讨会

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splatter

Simple simulation of single-cell RNA sequencing data

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Plant-Disease-Identification-using-CNN

Plant Disease Identification Using Convulutional Neural Network

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bioc-refcard

Bioconductor cheat sheet

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kent

UCSC Genome Browser source tree. Stable branch: "beta".

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deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors i...

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krakenuniq

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for...

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DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotat...

41   184   184  

dna2vec

dna2vec: Consistent vector representations of variable-length k-mers

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lung_cancer_biomarker

Bioinformatics Project. Trying to find out the most influential metabo...

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tutorial

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

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sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool

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amr

AMRFinderPlus - Identify AMR genes and point mutations, and virulence...

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PrimeKG

Precision Medicine Knowledge Graph (PrimeKG)

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ugene

UGENE is free open-source cross-platform bioinformatics software

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scde

R package for analyzing single-cell RNA-seq data

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biograkn

BioGrakn Knowledge Graph

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gcp-for-bioinformatics

GCP for Bioinformatics Researchers

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genomics

A collection of scripts and notes related to genomics and bioinformati...

50   171   171  

Clairvoyante

Clairvoyante: a multi-task convolutional deep neural network for varia...

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DnaChisel

:pencil2: A versatile DNA sequence optimizer

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chromVAR

chromatin Variability Across Regions (of the genome!)

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PPanGGOLiN

Build a partitioned pangenome graph from microbial genomes

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gfatools

Tools for manipulating sequence graphs in the GFA and rGFA formats

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pyani

Application and Python module for average nucleotide identity analyses...

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