Biology.md

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

• BIOINFORMATICS
• BIOSTATISTICS
• ECOLOGY
• GENOMICS
  • GWAS
• Org-BioJulia
• Org-JuliaBio
• NEUROSCIENCE
• Resources-Teaching

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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.
• 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.

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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.

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ECOLOGY

• Diversity.jl :: Diversity analysis package for Julia, with submodules containing standard ecological and other diversity measures.

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GENOMICS

• 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).
• 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.
• 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.
• TimeTrees.jl :: Phylogenetic tree type for julia.
• YARS.jl :: YARS communication for RNA/proteins.

GWAS

Genome Wide Association Study (GWAS)

• VarianceComponentTest.jl :: A Julia package for performing exact variance component tests in genome-wide association study (GWAS).

Resources

• 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.
• Data Analysis for Genomics : This is entirely in R-language but learners can use it to learn Julia.

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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.

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Org-JuliaBio

The GoogleGroups mailing list.

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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.
• SkullSegment.jl :: Macaque brain and skull extraction tools.
• SpikeSorter.jl :: Spike sorting tool for experimental neuroscientists.

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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.

• Common Bioinformatics Teaching Resources by Aidan Budd at EMBL.
• A google document listing Python for biologists resources by Lenny Teytelman (@lteytelman on twitter).
• Software Carpentry teaching material.
• Train online provides free courses on Europe's most widely used data resources, created by experts at EMBL-EBI and collaborating institutes.
• TrainingPhyloIntro :: Practical exercises and slides for teaching computational molecular evolution.
• capetown2014 :: Teaching material for EMBO Practical Course on Computational analysis of protein-protein interactions - From sequences to networks run in Cape Town 2014.
• course_EMBO_at_TGAC_PPI_Sep2015 :: Program and some material for EMBO Practical Course on computational analysis of protein-protein interactions: From sequences to networks, taking place at TGAC, Norwich, UK, Sep-Oct 2015.
• Ian Quigley's (@mucociliary on twitter) notes on teaching applied bioinformatics / compbio.
• Ubiquitous Genomics :: COMSE6998/ Class 2015 by Prof. Yaniv Erlich. The source is available on github.