walkthroughs

Noe: These walkthroughs only work on Linux

Download the data

$ lama_get_walkthrough_data # Downloads walkthrough data and scripts to current directory
$ cd lama_walkthroughs/
$ chmod u+x *.sh # make excecutable

Within lama_walkthroughs you should see some shell scripts and a data/ directory

The 3 interactive shell scripts perform various tasks. These can be run from the command line or just opening to get instructions.

Make a population average

$ ./population_average.sh 

This scripts shows the steps needed to get image metadata and to pad images all to the same size, which us required. Then it create a population average from 8 male E14.5 WT embryos.

Spatially-normalise wild type and mutant images to pre-made population average and atlas

$ ./spatially_normalise_data.sh

This script gets the mutant and wild type data registered into the same space as the population average. The script actually uses our E14.5 population average as it has an associated atlas

Run the stats pipeline

$ ./stats_with_BH_correction.sh

note: You must run spatailly_normalise_data.sh before running this script

This script run the statistical pipeline comparing the 8 wild types against each mutant line (one line in this case) as we only analyse one line, we apply FDR correction on the pvalues across all the organs (as opposed to across all the lines if we have multiple mutant lines - see [permutation based stats](Permutation based statistics)