Most popular bioinformatics repositories and open source projects

staramr

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

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configs

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

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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  

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

36   68   68  

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  

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  

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

27   67   67  

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

7   67   67  

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  

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  

bionode-ncbi

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

21   64   64  

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...

22   64   64  

singleCellHaystack

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

7   64   64  

obi

The Ontology for Biomedical Investigations

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