/BIDS-TP_Hackathon_2023

2023 BIDS mini-hackathon project

Primary LanguageR

BIDS-TP Hackathon 2023

Setup R environment

Install the following R packages using install.packages():

  1. tidyverse
  2. arrow
  3. spatstat
  4. spatstat.explore
  5. spatstat.model
  6. sf
  7. mgcv

Description of data

drive link for the data

data/TS2PL1_Cell_MasterDataTable.parquet

703 morphological features for 1,698,930 huh-7 hepatocyte cells. Each cell is contained in one of 9 fields of view in one of 384 wells.

Each well was either uninfected, or infected such that at the end of the assay at 48 hours it had been infected for between 8 and 48 hours.

Condition Number of cells 18 hours 300276 24 hours 248414 30 hours 242315 36 hours 213150 48 hours 149378 8 hours 307062 Uninfected 238335

Feature were generated using CellProfiler after fixing and staining cells with four different dyes (Hoe: hoechst, stains nuclei; ConA: Concanavalin A, stains membranes; Spike: stains SARS-CoV-2 Spike protein; and NP: stains SARS-CoV-2 N-protein) and then imaging with a confocal microscope. Features are named based on the

<feature_type>_

For instance

Cells_Intensity_MeanIntensityEdge_Spike

is the meain edge intensity of the Spike stain in the Cells objects

data/cell_clusters.parquet

Modularity based clustering of cells based on cellular phenotype into 239 clusters (median cluster size 7161).

Presentation