A.12: Free apps for bioinformatics

Mike’s Biostatistics Book · LibreTexts

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    From LibreTexts, under CC BY-NC-SA 4.0, as the source states it; its equations are written in TeX, which the PDF shows typeset. This page at LibreTexts.

    Mike’s recommended free and/or open-source apps for bioinformatics on macOS or Windows 11 PCs.

    Note:

    Chrome OS users: If your device is Intel-based, then it is possible to install many of the apps (or equivalents) listed via activating LINUX on your device. This route is only advisable if you are willing and able to do some pretty serious installation work.

    Statistics

    R Core Team (2024). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

    Python programming language and libraries: panda, Numby, Scipy, Matplotlib, Biopython, PySB, and others

    Mathematics software

    GNU Octave, free and open source, uses similar programming syntax to MATLAB, https://octave.org/

    SageMATH, python based, free and open source alternative to MATLAB and Wolfram Mathematica, https://www.sagemath.org/

    Image, Drawing, Concept & Mind maps, Flow charts

    Newt Editor, a free, web based, open source viewer and editor for biology pathways, https://newteditor.org/index.html

    Draw.io, used to create work flows, mind maps, https://app.diagrams.net/

    FreeCAD, open source “parametric 3D modeler”, https://www.freecad.org/

    GIMP, GNU Image Manipulation Program, at https://www.gimp.org/

    ImageJ2, JAVA-based, https://imagej.net/software/imagej2/

    Krita, free and open source painting program, https://krita.org/en/

    Preview, macos only

    Video editor

    Shortcut, at https://shotcut.org/

    Handbrake, at https://handbrake.fr/

    Screen recording, Video streaming

    OBS Studio, at https://obsproject.com/

    QuickTimePlayer, macos only

    Office suite (compatible with Microsoft Word)

    LibreOffice, at https://www.libreoffice.org/

    Reference manager

    Zotero, https://www.zotero.org/

    Digital Notebook

    Jupyter Lab and Notebooks, python based, web-based computational notebooks. In addition to python, Jupyter supports Julia and R Programming languages as well as Cytoscape, GNU Octave, SageMATH and other software. https://docs.jupyter.org/en/latest/index.html

    OneNote, at https://www.onenote.com/

    Bioinformatics tools

    Bioconductor, at https://www.bioconductor.org/

    Unipro UGENE, at http://ugene.net/

    Cytoscape, at https://cytoscape.org/

    MEGA, at https://www.megasoftware.net/

    Coding IDE and code editor

    Jupyter Lab

    Visual Studio with Python application, Community edition, https://visualstudio.microsoft.com/vs/features/python/

    Posit team (2024). RStudio: Integrated Development Environment for R. Posit Software, PBC, Boston, MA URL http://www.posit.co/.

    This page titled A.12: Free apps for bioinformatics was last modified on Wed, 04 Sep 2024 04:40:28 GMT and is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Michael R Dohm via source content that was edited to the style and standards of the LibreTexts platform.