docs: Remove the `eval: False` Quarto directive from README shell command blocks.

docs: clarify report reproduction steps by adding `renv::restore()` instructions and separating R and shell commands.

Remove pak from dependencies

fix README

Remove BiocParallel setup

Add initial project script

Add report and analysis files

Ignote HTML output

add packages to lockfile

Add BiocParallel to Rprofile

First commit