Skip to content

Latest commit

 

History

History
executable file
·
190 lines (149 loc) · 15 KB

Biology.md

File metadata and controls

executable file
·
190 lines (149 loc) · 15 KB
Raw

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

  • COBRA.jl :: COnstraint-Based Reconstruction and Analysis, used to perform COBRA analyses such as Flux Balance Anlysis (FBA), Flux Variability Anlysis (FVA), or any of its associated variants such as distributedFBA.

API's

  • BioServices.jl :: Julia interface to APIs for various bio-related web services

BIOINFORMATICS

  • Bio.jl :: Bioinformatics and Computational Biology Infrastructure for Julia. Wiki documentation of core features
  • Circuitscape.jl :: The Julia implementation of the Circuitscape lib in Python that uses electronic circuit theory to solve problems in landscape ecology.
  • EMIRT.jl :: Electron Microscopy Image Reconstruction Toolbox using julia language.
  • MIToS.jl.
  • 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.
  • openBF :: A finite-volume solver for elastic arterial networks.
  • Pipelines.jl :: A lightweight Julia package for computational pipelines and workflows.
  • 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
  • Bioinformatics.jl :: Helper functions for bioinformatics and rosalind.info problems.
  • NormalizeQuantiles.jl :: implements quantile normalization

BIOMEDICINE

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.
  • GBIF.jl :: Functions and types to access GBIF data from Julia
  • FishABM.jl :: An agent based life cycle model for managed fisheries.
  • EcologicalNetwork.jl :: Measure various aspects of the structure of ecological networks in Julia.
  • SpatialEcology.jl :: Julia framework for spatial ecology - data types and utilities

Agronomy and Forest Modelling

  • LeafAreaIndex.jl :: Package to calculate Leaf Area Index from Hemisperical Images.
  • LAIscript :: scripts to automatically run LAI calculations with ODBC link to custom database.

Aquatic Ecology

  • Iceberg.jl :: Ice-seawater interface calculations using level set methods.
  • TEOS.jl :: Julia wrapper for TEOS-10 Gibbs Seawater Oceanographic Toolbox.

GENOMICS

  • BioAlignments.jl :: Sequence alignment tools in BioJulia
  • BioArgParse.jl :: Extension to 'ArgParse.jl', enabling parsing of command line parameters to types in 'Bio.jl'.
  • BioFeatures.jl.
  • BioSeq.jl :: Julia's package for working on Bioinformatics with DNA, RNA and Protein Sequences.
  • 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.
  • GenomeGraphs.jl :: A modern genomics framework for julia
  • GenomicTiles.jl
  • Gillespie.jl :: Stochastic Gillespie-type simulations using Julia.
  • 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.
  • IntervalTrees.jl :: A data structure for efficient manipulation of sets of intervals.
  • MerCounting.jl :: Kmer counting algorithms and count-data utilities for the BioJulia framework
  • 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.
  • Phylogenetics.jl :: The Julia package for analysis of evolution and phylogeny.
  • 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.
  • 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.
  • MendelBase.jl :: contains the base functions of OpenMendel.
  • SnpArrays.jl :: provides utilities for handling compressed storage of biallelic SNP (Single-Nucleotide Polymorphism) data.
  • 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

Molecular Biology

  • EvoDuplexes.jl :: A Julia package to fold all local and long-range RNA duplexes.

DNA Sequencing

Single-Cell Sequencing

  • 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.

MIOCROSCOPY

NEUROSCIENCE

  • BrainWave.jl :: Julia functions to process electroencephalographic (EEG) recordings.
  • 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.
  • EEG.jl :: Process EEG files in Julia.
  • NEAT.jl :: Julia implemention of NEAT (NeuroEvolution of Augmenting Topologies) algorithm.
  • NeuroAnalysis.jl :: Julia package for neural signal analysis.
  • NeuronBuilder :: Builds conductance based neural networks iteratively, from ion channels and synapses.
  • 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.

PHARMACOLOGY

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.