Unverified Commit 89f5eb3c authored by ॥ स्वक्ष ॥'s avatar ॥ स्वक्ष ॥ Committed by GitHub

Merge pull request #182 from Sov-trotter/dev-bio

Updates for BioJulia
parents b04a53c9 73396c25
**Bioinformatics, genomics, agriculture, food science, medicine, genetic engineering, etc...**
+ [API's](#api's)
+ [BIOINFORMATICS](#bioinformatics)
+ [BIOMEDICINE](#biomedicine)
+ [BIOSTATISTICS](#bioinformatics)
......@@ -21,6 +22,12 @@
----
# API's
+ [BioServices.jl](https://github.com/BioJulia/BioServices.jl) :: Julia interface to APIs for various bio-related web services
----
# BIOINFORMATICS
+ [Bio.jl](https://github.com/BioJulia/Bio.jl) :: Bioinformatics and Computational Biology Infrastructure for Julia. Wiki documentation of [core features](https://github.com/BioJulia/Bio.jl/wiki/core-features)
+ [Circuitscape.jl](https://github.com/tanmaykm/Circuitscape.jl) :: The Julia implementation of the [Circuitscape lib in Python](http://www.circuitscape.org/) that uses electronic circuit theory to solve problems in landscape ecology.
......@@ -70,6 +77,7 @@
----
# GENOMICS
+ [BioAlignments.jl](https://github.com/BioJulia/BioAlignments.jl) :: Sequence alignment tools in BioJulia
+ [BioArgParse.jl](https://github.com/Ward9250/BioArgParse.jl) :: Extension to 'ArgParse.jl', enabling parsing of command line parameters to types in 'Bio.jl'.
+ [BioFeatures.jl](https://github.com/nw11/BioFeatures.jl).
+ [BioSeq.jl](https://github.com/BioJulia/BioSeq.jl) :: Julia's package for working on Bioinformatics with DNA, RNA and Protein Sequences.
......@@ -79,12 +87,14 @@
+ [FastaIO.jl](https://github.com/carlobaldassi/FastaIO.jl) :: Utilities to read/write FASTA format files in Julia.
+ [FusionDirect.jl](https://github.com/OpenGene/FusionDirect.jl) :: Detect gene fusion directly from raw fastq files.
+ [GenomeAnnotations.jl](https://github.com/nw11/GenomeAnnotations.jl) :: Manage Local Genome Annotation files.
+ [GenomeGraphs.jl](https://github.com/BioJulia/GenomeGraphs.jl) :: A modern genomics framework for julia
+ [GenomicTiles.jl](https://github.com/nw11/GenomicTiles.jl)
+ [Gillespie.jl](https://github.com/sdwfrost/Gillespie.jl) :: Stochastic Gillespie-type simulations using Julia.
+ [gtf-parse-off](https://github.com/dcjones/gtf-parse-off) :: Experiments with parsing gene transfer format (GTF).
+ [HTSLIB.jl](https://github.com/OpenGene/HTSLIB.jl) :: A julia wrapper of htslib for accessing common high-throughput sequencing data file formats such as BAM/SAM files.
+ [HyperNEAT.jl](https://github.com/kzahedi/HyperNEAT.jl) :: A generative encoding for evolving ANN based on the NeuroEvolution of Augmented Topologies (NEAT) algorithm for evolutionary computation.
+ [IntervalTrees.jl](https://github.com/BioJulia/IntervalTrees.jl) :: A data structure for efficient manipulation of sets of intervals.
+ [MerCounting.jl](https://github.com/BioJulia/MerCounting.jl) :: Kmer counting algorithms and count-data utilities for the BioJulia framework
+ [LCS.jl](https://github.com/WestleyArgentum/LCS.jl) :: A package for finding longest common and longest contiguous subsequences.
+ [OBC.jl](https://github.com/binarybana/OBC.jl) :: Optimal Bayesian classification for RNA-Seq data.
+ [OpenGene.jl](https://github.com/OpenGene/OpenGene.jl) :: OpenGene core library in Julia.
......@@ -119,7 +129,7 @@ __Genome Wide Association Study (GWAS)__
###### Resources
+ Wikipedia's [list of RNA-Seq bioinformatics tools](http://en.wikipedia.org/wiki/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](https://genomicsclass.github.io/book/) : This is entirely in R-language but learners can use it to learn Julia.
+ [BioTutorials](https://github.com/BioJulia/BioTutorials) : Tutorial Notebooks of BioJulia
## Molecular Biology
+ [EvoDuplexes.jl](https://github.com/timbitz/EvoDuplexes.jl) :: A Julia package to fold all local and long-range RNA duplexes.
......
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