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.

Links

https://github.com/bigdatagenomics/adam

http://bdgenomics.org/

Azimuth: intelligent selection of CRISPR/Cas9 guide strands

ML Techniques

Gradient-boosted regression trees

Links

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

Links

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

Links

https://github.com/CellCognition/cecog

http://cellcognition.org/about

CellProfiler: open-source cellular image analysis software.

Links

http://cellprofiler.org

https://github.com/CellProfiler/CellProfiler

DISIMRank: MATLAB Gaussian Process Transcription Factor Target Ranking Toolbox

Links

https://github.com/SheffieldML/disimrank

https://github.com/lawrennd/disimrank

nnNorm

Links

https://www.bioconductor.org/packages/release/bioc/html/nnNorm.html

VariantSpark: Apply Spark-based Machine Learning methods to whole-genome variant information

Links

https://github.com/BauerLab/VariantSpark

https://github.com/BauerLab/VariantSpark/blob/master/doc/publications/BigData2015/Big%20Data2015_O'Brien.R1.pdf