docs/pipeline.md

In caitlinjones/halo: Development version of the package 'halo', which analyzes and visualizes Halo data

final_pipeline.R

Main pipeline input is a single configuration file containing all parameters needed for all analyses to be run.

Step 1:

• Study configuration and study meta data is read and parsed.
• If annotations_file is not specified in study config, all files in annotations_dirs will be parsed and stored.
• If --markExclusions is used and rawDataDir or rawDataFiles is provided, an EXCLUDE column will be added to data indicating which cells to ignore during analysis. A cell is determined to be excluded based on information in:
  • *FOVannotations.xlsx in meta data directory
  • files in driftDir or driftFiles
  • Halo annotation boundary files in annotationsDirs or annotationsFile Output files will be written to dataDir and files will be named with '_Excl' appended to the associated raw data file name.

caitlinjones/halo documentation built on May 7, 2019, 8 a.m.