Bioinformatics, genomics, agriculture, food science, medicine, genetic engineering, etc...
- 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.
- 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.
- 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.
- Ensemble.jl :: Ensemble Samplers for Julia.
- FastaIO.jl :: Utilities to read/write FASTA format files in Julia.
- GenomicTiles.jl
- gtf-parse-off :: Experiments with parsing gene transfer format (GTF).
- 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.
- Pagel.jl :: Detect correlated evolution on phylogenies.
- Pathogen.jl :: Utilities to simulate and perform inference of disease dynamics.
- 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.
- StatGenData.jl :: Statistical analysis of genomic data.
- Wikipedia's list of RNA-Seq bioinformatics tools, not many of which are in Julia but depending on the language, they may have an API.
- YARS.jl :: YARS communication for RNA/proteins.
- Data Analysis for Genomics : This is entirely in R-language but learners can use it to learn Julia.
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
Their GoogleGroups mailing list.
- 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.
- NeuroAnalysis.jl :: Julia package for neural signal analysis.
- SkullSegment.jl :: Macaque brain and skull extraction tools.
- SpikeSorter.jl :: Spike sorting tool for experimental neuroscientists.