569 Open source projects that are alternatives of or similar to Bio

Bioinformatics containers

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

Python library to handle Gene Ontology (GO) terms

compacted de Bruijn graph construction in low memory

Exact Tandem Repeat Finder (not a TRF replacement)

Randomly subsample sequencing reads to a specified coverage

A collaboratively written review paper on deep learning, genomics, and precision medicine

课题组每周研讨会

Modular and universal bioinformatics

The Chemistry Development Kit

Plant image analysis using OpenCV

🌈Scaffold genome sequence assemblies using linked read sequencing data

A lightweight immune repertoire browser

Accurate sample inference from amplicon data with single nucleotide resolution

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Post-analysis of immune repertoire sequencing data

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

An analysis and visualization platform for 'omics data

Structural variant and indel caller for mapped sequencing data

Parser and database to index the terpene profile of different strains of Cannabis from online databases

COBRApy is a package for constraint-based modeling of metabolic networks.

Interactive network visualization in Python and Dash, powered by Cytoscape.js

A friendly next-generation interface for Genomic data discovery powered by InterMine

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

GO enrichment with python -- pandas meets networkx

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics

Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R

Genome inference from a population reference graph

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files

UNCURL is a tool for single cell RNA-seq data analysis.

👁 Python library to plot DNA sequence features (e.g. from Genbank files)

Fast genome-wide functional annotation through orthology assignment

A tutorial on methods of 16S analysis with QIIME 1

A full spaCy pipeline and models for scientific/biomedical documents.

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

LAMBDA – the Local Aligner for Massive Biological DatA

Single-Cell Analysis in Python. Scales to >1M cells.

PHANOTATE: a tool to annotate phage genomes.

MyGene.info: A BioThings API for gene annotations

Estimate metagenomic coverage and sequence diversity

Highly adaptable common interface for proteomics search and de novo engines

Real-time species-typing visualisation for nanopore data.

🐣 locally query the ncbi taxonomy

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Aim to be the bioinformatics repository with more and newer packages

Javascript full-stack framework for Big Data visualisation and analysis

This library tackles the construction and efficient execution of computational chemistry workflows

Detection of NCLDV signatures in 'omic data

Bioinformatics Workbook repository

Biological sequences for the julia language

Development repository for the Bioconductor package 'mixOmics '

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

The uncompromising Snakemake code formatter

Sample search by metadata and features