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