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ggsgBioinformatics, genomics, agriculture, food science, medicine, genetic engineering, etc...

  • BioMedQuery.jl :: Utilities for interacting with different BioMedical Databases and APIs provided by the National Library of Medicine (NLM).

BIOINFORMATICS

  • Circuitscape.jl :: The Julia implementation of the Circuitscape lib in Python that uses electronic circuit theory to solve problems in landscape ecology.
  • EEG.jl :: Process EEG files in Julia.
  • EMIRT.jl :: Electron Microscopy Image Reconstruction Toolbox using julia language.
  • MIToS.jl.
  • Rosalind.jl :: A bioinformatics library for solving problems from rosalind.info.
  • smoothlife-jl :: an implementation of the SmoothLife algorithm in Julia.
  • taxize.jl :: A taxonomic toolbelt for Julia.
  • Crispulator.jl :: A discrete simulation tool for designing pooled genetic screens

BIOSTATISTICS

  • pedigree.jl :: Pedigree extractors and representation as a Julia type with two integer members, sire and dam. A parent not in the pedigree is coded as 0.
  • ROC.jl :: Receiver Operating Characteristic (ROC) Curve for Julia Language.

ECOLOGY

  • Diversity.jl :: Diversity analysis package for Julia, with submodules containing standard ecological and other diversity measures.
  • FishABM.jl :: An agent based life cycle model for managed fisheries.

GENOMICS

  • BioArgParse.jl :: Extension to 'ArgParse.jl', enabling parsing of command line parameters to types in 'Bio.jl'.
  • BioFeatures.jl.
  • BismarkSummary.jl :: Basic summary of multiple Bismark runs.
  • COSMIC.jl :: Data analysis engine for COSMIC written in Julia.
  • Ensemble.jl :: Ensemble Samplers for Julia.
  • FastaIO.jl :: Utilities to read/write FASTA format files in Julia.
  • FusionDirect.jl :: Detect gene fusion directly from raw fastq files.
  • GenomeAnnotations.jl :: Manage Local Genome Annotation files.
  • GenomicTiles.jl
  • gtf-parse-off :: Experiments with parsing gene transfer format (GTF).
  • HTSLIB.jl :: A julia wrapper of htslib for accessing common high-throughput sequencing data file formats such as BAM/SAM files.
  • HyperNEAT.jl :: A generative encoding for evolving ANN based on the NeuroEvolution of Augmented Topologies (NEAT) algorithm for evolutionary computation.
  • LCS.jl :: A package for finding longest common and longest contiguous subsequences.
  • OBC.jl :: Optimal Bayesian classification for RNA-Seq data.
  • OpenGene.jl :: OpenGene core library in Julia.
  • Pagel.jl :: Detect correlated evolution on phylogenies.
  • Pathogen.jl :: Utilities to simulate and perform inference of disease dynamics.
  • PedModule.jl :: Geno-type pedigree module.
  • PhyloNetworks.jl :: A Julia package for statistical inference, data manipulation and visualization of phylogenetic networks.
  • PhyloTrees.jl :: Phylogenetic tree simulation.
  • PlmDCA :: Pseudo Likelihood Maximization for protein in Julia.
  • ProgressiveAligner.jl :: Progressive alignment scripts for protein sequences.
  • PseudoGenomes.jl :: Read alleles without a VCF parser.
  • PureSeq.jl :: Code for the Pure-seq project.
  • SeqUtils.jl :: Seqencing analysis Utilities for Julia.
  • seqhax.jl :: yet another NGS command.
  • SpeedDate.jl :: A simple tool for the estimation of coalescence times between sequences.
  • TimeTrees.jl :: Phylogenetic tree type for julia.
  • VariantCall.jl.
  • XSim.jl :: A fast and user-friendly tool to simulate sequence data and complicated pedigree structures.
  • YARS.jl :: YARS communication for RNA/proteins.

GWAS

Genome Wide Association Study (GWAS)

  • AlignmentStatistics.jl :: A package for statistical analyses of sequence alignments.
  • JWAS.jl :: An open-source software tool written in Julia for Bayesian multiple regression methods applied to genome-wide association studies and genomic prediction.
  • StatGenData.jl :: Statistical analysis of genomic data.
  • VarianceComponentTest.jl :: A Julia package for performing exact variance component tests in genome-wide association study (GWAS).
Resources

Org-BioJulia

Their GoogleGroups mailing list and list of packages under the Org:

  • Bio.jl :: Bioinformatics and Computational Biology Infrastructure for Julia. Wiki documentation of core features
  • BioSeq.jl :: Julia's package for working on Bioinformatics with DNA, RNA and Protein Sequences.
  • IntervalTrees.jl :: A data structure for efficient manipulation of sets of intervals.
  • Phylogenetics.jl :: The Julia package for analysis of evolution and phylogeny.

Org-JuliaBio

The GoogleGroups mailing list.

NEUROSCIENCE

  • CodeNeuro :: Bringing neuroscience and data science together.
  • DCEMRI.jl :: A Fast, Validated Toolkit for Dynamic Contrast Enhanced MRI Analysis. A paper on the code is in press at PeerJ.
  • ElectroJulia.jl :: Julia functions to process electroencephalographic recordings.
  • NEAT.jl :: Julia implemention of NEAT (NeuroEvolution of Augmenting Topologies) algorithm.
  • NeuroAnalysis.jl :: Julia package for neural signal analysis.
  • OpenEphysLoader.jl :: A set of tools to load data written by the Open Ephys GUI.
  • SkullSegment.jl :: Macaque brain and skull extraction tools.
  • SpikeSorter.jl :: Spike sorting tool for experimental neuroscientists.

Resources-Teaching

NotaBene:: Some resources and teaching aids listed here are not Julia language specific but you may be able to find something common and useful that can be reused and shared with attribution if it is CC-licensed.