Most popular bioinformatics repositories and open source projects

GeneFuse

Gene fusion detection and visualization

57   107   107  

PhysiCell

PhysiCell: Scientist end users should use latest release! Developers p...

73   107   107  

genome_updater

Bash script to download/update snapshots of files from NCBI genomes re...

12   107   107  

RNAlysis

RNA sequencing analysis software

13   107   107  

spacegraphcats

Indexing & querying large assembly graphs -- in space, no one can hear...

14   106   106  

plass

Protein-Level ASSembler (PLASS): sensitive and precise protein assembl...

11   106   106  

fermikit

De novo assembly based variant calling pipeline for Illumina short rea...

23   105   105  

saber

Saber is a deep-learning based tool for information extraction in the...

17   105   105  

swarm

A robust and fast clustering method for amplicon-based studies

21   105   105  

gencore

Generate duplex/single consensus reads to reduce sequencing noises and...

31   105   105  

dbsnp

dbSNP

48   105   105  

biocypher

A unifying framework for biomedical research knowledge graphs

14   105   105  

mygene.info

MyGene.info: A BioThings API for gene annotations

21   104   104  

biojava-tutorial

:book::books:An introductory tutorial for BioJava

40   104   104  

fastqp

Simple FASTQ quality assessment using Python

16   103   103  

molgenis

MOLGENIS - for scientific data: management, exploration, integration a...

101   103   103  

fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes...

23   103   103  

cLoops

Accurate and flexible loops calling tool for 3D genomic data.

19   102   102  

biojupies

Automated generation of tailored bioinformatics Jupyter Notebooks via...

27   102   102  

Clair

Clair: Exploring the limit of using deep neural network on pileup data...

12   102   102  

bio-transformers

bio-transformers is a wrapper on top of the ESM/Protbert model, traine...

25   102   102  

redundans

Redundans is a pipeline that assists an assembly of heterozygous/polym...

19   102   102  

swne

Similarity Weighted Nonnegative Embedding (SWNE), a method for visuali...

21   101   101  

BioFSharp

Open source bioinformatics and computational biology toolbox written i...

33   101   101  

dolphinnext

A graphical user interface for distributed data processing of high thr...

22   101   101  

hAMRonization

Parse multiple Antimicrobial Resistance Analysis Reports into a common...

21   100   100  

nightingale

Data visualisation web components for the life sciences.

29   100   100  

deepsignal

Detecting methylation using signal-level features from Nanopore sequen...

20   99   99  

DEEPScreen

DEEPScreen: Virtual Screening with Deep Convolutional Neural Networks...

34   99   99  

Workshop

课题组每周研讨会

37   99   99  

perbase

Per-base per-nucleotide depth analysis

12   99   99  

best

Bam Error Stats Tool (best): analysis of error types in aligned reads.

5   99   99  

GenomicConsensus

PacBio® variant and consensus caller

43   98   98  

grabseqs

A utility for easy downloading of reads from next-gen sequencing repos...

14   98   98  

block-aligner

SIMD-accelerated library for computing global and X-drop affine gap pe...

6   98   98  

strobealign

Aligns short reads using dynamic seed size with strobemers

13   98   98  

NucleoATAC

nucleosome calling using ATAC-seq

29   97   97  

Terpene-Profile-Parser-for-Cannabis-Strains

Parser and database to index the terpene profile of different strains...

20   97   97  

Plant-Disease-Identification-using-CNN

Plant Disease Identification Using Convulutional Neural Network

38   97   97  

chewBBACA

BSR-Based Allele Calling Algorithm

23   97   97  

ga4gh-server

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED...

93   96   96  

cute-nucleotides

Cute tricks for SIMD vectorized binary encoding and decoding of nucleo...

4   96   96  

eager

A fully reproducible and state-of-the-art ancient DNA analysis pipelin...

69   96   96  

pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for ge...

3   96   96  

clusterflow

A pipelining tool to automate and standardise bioinformatics analyses...

26   95   95  

philosopher

A complete toolkit for shotgun proteomics data analysis

17   95   95  

RNArtist

RNArtist allows you to design and paint your RNA 2D structures interac...

9   95   95  

ccs

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Re...

31   94   94  

kalign

A fast multiple sequence alignment program.

26   94   94  

fastq.bio

An interactive web tool for quality control of DNA sequencing data

12   93   93