Kim lab analyses 202410: README/Introduction

1 Introduction

The R markdown documents in this directory are intended to provide a complete accounting of the analyses performed in the preparation of

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I assume that if anyone ever reads this, s/he is looking for the source of the data, figures, and tables from that paper and to see if the methods employed to generate them are good, bad, indifferent, or garbage. These documents are being generated by a singularity container which provides the input count tables (Once we have accessions, I will make a companion which is able to create them), sample sheets, input documents, and all the software used to process them. The overal configuration of the container is contained in the toplevel .yml file and provides the base OS (Debian stable) and the scripts used to install the software. ‘local/bin/setup_debian.sh’ handles the base container; ‘local/bin/setup_hpgltools.sh’ sets up R, bioconductor, and my package ‘hpgltools’, and ‘local/bin/runscript’ is the script run if one invokes the container without any arguments; when run it uses the various installed R packages to ‘render’ the Rmd files in /data to freshly created html. This README is the first document rendered.

2 Figure/Table locations

As of 20240919, Maria Adelaida kindly sent me the putatively final set of figures/tables. I am going to lay out the location in the html logs and their Rmd parents where these may be found. If you wish to play along, make sure you run the entire 01datastructures.Rmd.

Also, this container is automatically regenerated and rerun when I make changes; so one may just go here to play along (that is where I am going to hunt down the figures/tables):

https://containerbook.umiacs.io/