Biology

Bioinformatics, genomics, agriculture, food science, medicine, genetic engineering, etc., in Julia.

Accessing biology databases¶

BioJulia/BioFetch.jl : Easily fetch biological sequences from online sources. Currently supports Entrez (NCBI) Nucleotide and Protein databases, as well as UniProt and Ensembl.
BioJulia/BioServices.jl : Julia interface to APIs for various bio-related web services.
JuliaHealth/BioMedQuery.jl : Julia utilities to process and save results from BioMedical databases/APIs.
JuliaHealth/PubChemCrawler.jl : Utilities to programmatically query the PubChem database.
JuliaHealth/PubMedMiner.jl : Julia package for studying co-occurrences in PubMed articles.
wherrera10/DailyMed.jl : Interface to the REST functions of the National Library of Medicine's DailyMed database.
wherrera10/RxNav.jl : Julia interface to the National Library of Medicine's online pharmaceutical RxNav API.

BioJulia/MMTF.jl : The Macromolecular Transmission Format (MMTF) is a new compact binary format to transmit and store biomolecular structures for fast 3D visualization and analysis.
carlobaldassi/FastaIO.jl : Utilities to read/write FASTA format files in Julia.
diegozea/MIToS.jl : Mutual Information Tools for protein Sequence analysis in Julia.
farr/Ensemble.jl : Stochastic samplers based on the "stretch move" for ensembles of walkers.
oheil/NormalizeQuantiles.jl : implements quantile normalization
pagnani/PlmDCA.jl : Pseudo Likelihood Maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences.
reworkhow/XSim.jl : A fast and user-friendly tool to simulate sequence data and complicated pedigree structures.
vanOosterhoutLab/SpeedDate.jl : A utility for rapidly estimating coalescence times between sequences.

Packages in the BioJulia organization.

BioJulia/BED.jl : I/O and utilities for the BED file format.
BioJulia/BioAlignments.jl : Sequence alignment tools in BioJulia.
BioJulia/BioSequences.jl : Biological sequences for the julia language.
BioJulia/BioStructures.jl : A Julia package to read, write and manipulate macromolecular structures (particularly proteins).
BioJulia/BioSymbols.jl : Nucleic and amino acid primitive types.
BioJulia/BioTools.jl : Interfaces to common external biological tools from julia scripts and programs (e.g. BLAST).
BioJulia/FASTX.jl : Parse and process FASTA and FASTQ formatted files of biological sequences.
BioJulia/GeneticVariation.jl : types and methods for working with genetic variation.
BioJulia/GenomeGraphs.jl : A modern genomics framework for julia
BioJulia/GenomicFeatures.jl : utilities for working with interval based genomic annotations.
BioJulia/IntervalTrees.jl : A data structure for efficient manipulation of sets of intervals.
BioJulia/KmerAnalysis.jl : Kmer counting algorithms and count-data utilities for the BioJulia framework.
BioJulia/XAM.jl : Parse and process SAM and BAM formatted alignment map files.
EcoJulia/Microbiome.jl : manipulating and analyzing microbiome and microbial community data.

Wikiedia: Phylogenetics. Phylogenic trees are evolution trees deduced from biosequences.

cecileane/PhyloPlots.jl : Display utilities for phylogenetic trees and networks.
crsl4/PhyloNetworks.jl : A Julia package for statistical inference, data manipulation and visualization of phylogenetic networks.
EcoJulia/Phylo.jl : Simple phylogenetic trees in Julia to work with Diversity.jl.
jangevaare/PhyloTrees.jl : Phylogenetic tree simulation.

Wikipedia: GWAS
Wikipedia: list of RNA-Seq bioinformatics tools, not many of which are in Julia but depending on the language, they may have an API.
Data Analysis for Genomics : with R programming language but FYI.

BioJulia/PopGen.jl : Population Genetics in Julia.
OpenMendel/MendelBase.jl : contains the base functions of OpenMendel.
OpenMendel/SnpArrays.jl : provides utilities for handling compressed storage of biallelic SNP (Single-Nucleotide Polymorphism) data.
reworkhow/JWAS.jl : An open-source software tool for Bayesian multiple regression methods applied to genome-wide association studies (GWAS) and genomic prediction.

LCSB-BioCore/COBREXA.jl : constraint-based reconstruction and analysis tools for exa-scale metabolic models in Julia. It uses JuMP to formulate optimization problems.
stelmo/Escher.jl : escherplot is a Makie.jl recipe that plots maps of metabolic models.

bicycle1885/CellFishing.jl : CellFishing.jl (cell finder via hashing) is a tool to find similar cells of query cells based on their transcriptome expression profiles, a.k.a. single-cell sequencing.

ahnlabb/BioformatsLoader.jl : load images using bioformats based on JavaCall.jl.
bionanoimaging/FourierTools.jl : Tools for working with Fourier (Frequency) space. JuliaCon 2021 video
RainerHeintzmann/PointSpreadFunctions.jl : Toolbox for calculating optical point spread functions (PSFs).
RainerHeintzmann/View5D.jl : a Java-based viewer for up to 5-dimensional data.
roflmaostc/DeconvOptim.jl : A multi-dimensional, high performance deconvolution framework written in Julia Lang for CPUs and GPUs. JuliaCon 2021 video
timholy/ImagineFormat.jl : Read .imagine light sheet microscopy file formats in Julia.
tlnagy/MicroscopyLabels.jl : Embed annotations in your microscopy images.

davidssmith/DCEMRI.jl : A Fast, Validated Toolkit for Dynamic Contrast Enhanced MRI Analysis. A paper on the code is in press at PeerJ.
Experica/NeuroAnalysis.jl : Julia package for neural signal analysis.
galenlynch/OpenEphysLoader.jl : A set of tools to load data written by the Open Ephys GUI.
rob-luke/Neuroimaging.jl : Process neuroimaging data using the Julia language.
sam81/BrainWave.jl : Julia functions to process electroencephalographic (EEG) recordings.

InPhyT/ICD_GEMs.jl : translate ICD-9 codes in ICD-10 and vice versa via the General Equivalence Mappings (GEMs). ICD stands for International Classification of Diseases.
INSIGNEO/openBF : A finite-volume solver for 1D elastic arterial blood flow networks.
JuliaHealth/DICOM.jl : Julia package for reading and writing DICOM (Digital Imaging and Communications in Medicine) files. JuliaHealth/DICOMClient.jl provides a Julia client for connecting to servers.
JuliaHealth/PharmaceuticalClassification.jl : Mappings between different systems for classifying medications.
PharmCat/ODMXMLTools.jl : a simple tool set for working with ODM-XML, a vendor-neutral, platform-independent format for exchanging and archiving clinical and translational research data and friends.