Most popular bioinformatics repositories and open source projects

ANANSE

Prediction of key transcription factors in cell fate determination usi...

13   71   71  

DeepMicrobes

DeepMicrobes: taxonomic classification for metagenomics with deep lear...

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staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFi...

22   70   70  

configs

Config files used to define parameters specific to compute environment...

211   70   70  

scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, s...

10   70   70  

CRISPRCasTyper

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons

11   70   70  

nanocompore

RNA modifications detection from Nanopore dRNA-Seq data

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vrs

Extensible specification for representing and uniquely identifying bio...

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sshash

A compressed, associative, exact, and weighted dictionary for k-mers.

9   69   69  

CUT-RUNTools-2.0

CUT&RUN and CUT&Tag data processing and analysis

54   69   69  

IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores...

9   68   68  

kmer-db

Kmer-db is a fast and memory-efficient tool for large-scale k-mer anal...

15   68   68  

butler

Butler is a framework for running scientific workflows on public and a...

19   68   68  

tibanna

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). I...

22   68   68  

bonsai

Bonsai: Fast, flexible taxonomic analysis and classification

11   68   68  

cogent3

Comparative Genomics Toolkit 3

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TileDB-VCF

Efficient variant-call data storage and retrieval library using the Ti...

13   68   68  

Drug-Drug-Interaction-Prediction

Drug-Drug Interaction Prediction Based on Knowledge Graph Embeddings a...

28   68   68  

fermi-lite

Standalone C library for assembling Illumina short reads in small regi...

21   67   67  

Qiime16sTutorial

A tutorial on methods of 16S analysis with QIIME 1

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ropebwt2

Incremental construction of FM-index for DNA sequences

5   67   67  

Palimpsest

An R package for studying mutational signatures and structural variant...

18   67   67  

yacrd

Yet Another Chimeric Read Detector

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ganon

ganon classifies short DNA sequences against large sets of genomic seq...

11   67   67  

CeleScope

Single Cell Analysis Pipelines

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compleasm

A genome completeness evaluation tool based on miniprot

2   67   67  

bionode-ncbi

Node.js module for working with the NCBI API (aka e-utils).

19   66   66  

bfc

High-performance error correction for Illumina resequencing data

13   66   66  

dna-nn

Model and predict short DNA sequence features with neural networks

7   66   66  

epiviz

EpiViz is a scientific information visualization tool for genetic and...

12   66   66  

NeoDTI

NeoDTI: Neural integration of neighbor information from a heterogeneou...

33   66   66  

VerifyBamID

VerifyBamID2: A robust tool for DNA contamination estimation from sequ...

14   66   66  

ontology-tutorial

Ontology Tutorial

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GFF3toolkit

Python programs for processing GFF3 files

26   66   66  

typedb-bio

TypeDB Bio: Biomedical Knowledge Graph

29   66   66  

SplitThreader

Explore rearrangements and copy-number amplifications in a cancer geno...

16   65   65  

libBigWig

A C library for handling bigWig files

25   65   65  

hypeR

An R Package for Geneset Enrichment Workflows

13   65   65  

quantQ

The repository for the Machine Learning and Big Data with kdb+/q book...

38   65   65  

mavis

Merging, Annotation, Validation, and Illustration of Structural varian...

13   65   65  

scaden

Deep Learning based cell composition analysis with Scaden.

25   65   65  

SumGNN

[Bioinformatics 2021] This is the repo for the paper `SumGNN: Multi-ty...

18   65   65  

dysgu

dysgu-SV is a collection of tools for calling structural variants usin...

8   65   65  

dash-tools

DashTools - Plotly Dash Command Line Tools - Create, Run and Deploy Te...

8   65   65  

wgbs_tools

tools for working with Bisulfite Sequencing data while preserving read...

20   65   65  

biobear

Work with bioinformatic files using Arrow, Polars, and/or DuckDB

1   65   65  

dna-traits

A fast 23andMe genome text file parser, now superseded by arv

5   64   64  

lambda

LAMBDA – the Local Aligner for Massive Biological DatA

19   64   64  

sample

Performs memory-efficient reservoir sampling on very large input files...

12   64   64  

scATAC-pro

A comprehensive tool for processing, analyzing and visulizing single c...

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