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A set of tools for the biologists who sequence RNA or watch cells in the Thomson Lab

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GhostOfMT

A set of tools for biologists who sequence RNA

To get started, make a folder called code in your home directory (~ on the command line, or on a mac click on finder, on the top bar select the go menu and the go to home), then download or clone this repository inside.

Includes:

  • Tutorials

    • Making gene lists from GO

    • Basic RNAseq EDA

    • Plotting Favorite Genes in a Time Series

    • ScaledBox & Overlay Heatmaps

    • Double-Color-Scheme Expression Heatmaps

    • SegReg and output analysis

    • ExpressionAtlas comparisons

    • Seahorse Data Processing

    • Mouse and Human Orthologs

    • PeakFinder

    • WGCNA (Maybe)

  • Tracking

    • Jython scripts for preprocessing images

    • Jython scripts for ImageJ cell tracking

    • Python scripts for processing tracking output

  • Data

    • Mouse and Human RNAseq Time Series from Barry, Schmitz et al (2017)

    • Carnegie Stage Comparisons

    • Gene lists

  • MiscR

    • Dumping ground for R code I can't organize
  • SegRegPar

    • A parallelized version of Ning Leng's Segmented Regression implementation, modified to fix problems with endpoints. Mostly the same as Rhonda's Trendy Package

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A set of tools for the biologists who sequence RNA or watch cells in the Thomson Lab

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