Gens Julia

Biology

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Bioinformatics, genomics, agriculture, food science in Julia.

For medicine, see health in Julia.

Accessing biology databases

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

Bioinformatics and genomics

  • Ensemble.jl) : Stochastic samplers based on the “stretch move” for ensembles of walkers.
  • FastaIO.jl : Utilities to read/write FASTA format files in Julia.
  • MIToS.jl : Mutual Information Tools for protein Sequence analysis in Julia.
  • 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.
  • NormalizeQuantiles.jl : implements quantile normalization
  • PdbTool.jl : An object-oriented Julia tool to parse PDB files and work with them.
  • PlmDCA.jl : Pseudo Likelihood Maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences.
  • SpeedDate.jl : A utility for rapidly estimating coalescence times between sequences.
  • XSim.jl : A fast and user-friendly tool to simulate sequence data and complicated pedigree structures.

BioJulia ecosystem

Packages in the BioJulia organization.

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

Phylogeny

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

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

Genomics

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

Metabolic networks

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

Molecular Biology

  • 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.

Microscopy and bioimages

Wikipedia: Microscopy

Graph View

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