Programming Languages used with Bioinformatics Tools

Bioinformatics researchers use a number of programming languages and libraries to analyze genomic data. Simple examples of code using common languages is shown in this folder. These languages and libraries include the following:

General Purpose Languages and Libraries

• Python: pip3, NumPy, SciPy, Matplotlib, Pandas
• R: dplyr, ggplot2, Shiny, Plotly, renv
• Julia: IJulia, SciML
• Java: Log4j 2, Mockito, Maven
• Scala: Breeze, Smile
• C++: Boost, STL, STXXL

Bioinformatics and Machine Learning Libraries

• R: randomForest, rPart, Bioconductor
• Python: PyTorch, NumPy, SciPy, Sci-kit Learn, TensorFlow (Keras). Jupyter
• Scala: Apache Spark ML Lib