359 Open source projects that are alternatives of or similar to macrel

Scripts to download genomes from the NCBI FTP servers

Java utilities for Bioinformatics

A powerful open source data warehouse system

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

A package for designing compact and comprehensive capture probe sets.

A modern genome browser built with JavaScript and HTML5.

Feature Annotation Location Description Ontology

A list of web-based interactive biological data visualizations.

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

An open-access bioinformatics text

Ten Quick Tips for Deep Learning in Biology

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Transcripts annotation and GO enrichment Fisher tests

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

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

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Python-based UCSC genome browser snapshot-taker and gallery-maker

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

🐳 Bio-dockers: dockerized bioinformatic tools

A library for manipulating bioinformatics sequencing formats in Apache Spark

Forward-time simulation in Python using fwdpp

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

Command line utility for manipulating Illumina-generated FastQ files.

Cellular Automata Simulator

Datastructures and algorithms for working with genetic variation

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

ganon classifies short DNA sequences against large sets of genomic sequences efficiently, with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and hierarchical classification, customized reporting and more

View biological networks via Cytoscape.js and sbgn-ml

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Bioconductor package for management of multi-assay data

Multilocus sequence typing by blast using the schemes from PubMLST

Nextflow basic tutorial for newbie users

A tool to plot significant regions of GWAS

Big Compute Learning Labs

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

gargammel is an ancient DNA simulator

A web application to visualize and edit pathway models

Improve the quality of a denovo assembly by scaffolding and gap filling

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Explore rearrangements and copy-number amplifications in a cancer genome

find large indels (in the blind spot between GATK/freebayes and SV callers)

A web application to visualize and edit the pathway models represented by SBGN Process Description Notation

Numerical Encoding for Human Genetic Variants

Julia Catalyst.jl importers for various reaction network file formats like BioNetGen and stoichiometry matrices

phenol: Phenotype ontology library

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

Identify phage regions in bacterial genomes for masking purposes

Bead-based single-cell atac processing

Explore gnomAD datasets on the web

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

A fast tool for hybrid genome assembly of long and short reads

Ultrafast sequence typing and gene detection from NGS raw reads

plant collections manager (desktop version)

Deep learning for Metagenome Assembly Error Detection

Spark VCF data source implementation for Dataframes

Examples to get started with IBM Functional Genomics Platform

Manhattan plot Generator

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface