High-throughput, Microscope-based Sorting to Dissect Cellular Heterogeneity NOTE that all code should be run from the directory the code is located in
contains monocle3 and batchelor github downloads for use in vcs_paclitaxel
sitemaps: htacquir.cfg files that were copied into the MetaMorph directory to load circular/elliptical site maps for various experiments journals: .pdf and .jnl files with the journals loaded into the Plate Acquisition dialog box for the experiments
activation_accuracy: code and .fcs files used to assess accuracy of activation activation_fourbin: code and .fcs files used to assess four bin activation activation_toxicity: code and .fcs files used to assess activation-induced toxicity activation_bulk_RNAseq: code and data used to analyze bulk RNA sequencing data
enrich2: configuration file used for enrich2 nls_imaging: Metamorph output files from analysis of NLS library pre-sort imaging data from Replicate 2, Technical Replicate 1 nls_post_sort_validation: Metamorph output files from analysis of the sorted NLS library nls_scores: code and enrich2 output used to calculate variant scores nls_validation: code and Metamorph output used to calculate variant NC ratios nls_prediction: code and data used to train and validate the NLS prediction model
imaging: imaging data from Experiment 1 (Visual Cell Sorting experiment) taken directly before Visual Cell Sorting scrnaseq: code and data used to analyze the single cell RNA sequencing data of Experiment 1 (cells treated with paclitaxel and sorted according to their nuclear shape) and Experiment 2 (cells treated with paclitaxel, activated as in experiment 1, and sorted into the same tube; i.e. left unseparated).