Machine Learning For Genomics
Collecting a list of open source machine learning projects solving genomic, molecular, systems, or cell biology problems.
Adam: genomics analysis platform using Apache Avro, Apache Spark and Parquet.
https://github.com/bigdatagenomics/adam
http://bdgenomics.org/
Azimuth: intelligent selection of CRISPR/Cas9 guide strands
Gradient-boosted regression trees
http://biorxiv.org/content/early/2015/06/26/021568
http://research.microsoft.com/en-us/projects/azimuth/
https://github.com/MicrosoftResearch/Azimuth
Basset: Deep convolutional neural networks for DNA sequence analysis
https://github.com/davek44/Basset
http://biorxiv.org/content/biorxiv/early/2015/10/05/028399.full.pdf
CellCognition: image analysis for fluorescence time-lapse microscopy
https://github.com/CellCognition/cecog
http://cellcognition.org/about
CellProfiler: open-source cellular image analysis software.
http://cellprofiler.org
https://github.com/CellProfiler/CellProfiler
DISIMRank: MATLAB Gaussian Process Transcription Factor Target Ranking Toolbox
https://github.com/SheffieldML/disimrank
https://github.com/lawrennd/disimrank
https://www.bioconductor.org/packages/release/bioc/html/nnNorm.html
VariantSpark: Apply Spark-based Machine Learning methods to whole-genome variant information
https://github.com/BauerLab/VariantSpark
https://github.com/BauerLab/VariantSpark/blob/master/doc/publications/BigData2015/Big%20Data2015_O'Brien.R1.pdf