QC for brentlab RNAseq data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  echo = TRUE,
  include = TRUE,
  eval = FALSE
)

library(brentlabRnaSeqTools)

Sending sets of images to the database

See the documentation in ?postCapsuleJpeg_batch. An example of calling this function is like so:

# note: there are no negative bioSampleNumbers. But I don't want to put 
# something in here that might get copied/pasted and sent to the database
bioSampleNumber = -1
image_dir = "/path/to/the/image_set_dir"
expected_number_of_images = 14

postCapsuleJpeg_batch(
  Sys.getenv("kn99_db_token"),
  bioSampleNumber,
  image_dir,
  expected_number_of_images
)

Retrieving a set of images

see the documentation in ?getCapsuleImageSet. An example of calling this function is like so:

bioSampleNumber = 440
# note: you do not want to keep images sets on your computer long term. Put them 
# somewhere that you can find, and then delete them when you are done. If you 
# need them in an hour, tomorrow, etc, you can always pull them again
out_dir = "~/Desktop/tmp_images"

getCapsuleImageSet(Sys.getenv("kn99_db_token"), bioSampleNumber, output_dir)