update readme content with overview, dependencies, scripts, data, etc

[lizzyjoan]

Summary

No code to review--just updates to the repo README!

Author Checklist

• This repository has a Lasseigne Lab ruleset configured.
  See instructions here.
• A singularity container has been created with all dependancies and the
  cap_container command has been included in each script using a container.
• All of the necessary scripts, dependencies, and inputs have been included
  in this pull request.
• Only files relevant to this change are included; no temporary, generated,
  or unrelated files are part of this pull request. Use .gitignore to prevent
  irrelevant files from accidentally being included.
• Results have been reproduced and verified with lasseignelab and
  default environments by running the job until two consecutive runs produce
  the same results. Code comments (per script) have been added for
  non-reproducible scripts. Include information about why the script is not
  reproducible.
• All automated code checks have passed. The "All checks have passed"
  message should show in the GitHub pull request status box above the
  "Merge pull request" button.
• No merge conflicts exist. Merge conflicts are indicated by the "This
  branch has conflicts that must be resolved" message in the GitHub pull
  request status box above the "Merge pull request" button.
• Primary and secondary reviewers have been requested to review this
  pull request.

Self/Peer Review Checklist (Coding Guidelines)

• Meaningful variable and function names
• File header comments
• Function comments
• In-line comments summarize logical sections of code by concisely explaining
  why, not what the code is doing. Avoid excessive or redundant commenting.
• Random seed is set
• Reasonable processing time for each job or script is specified
• All outputs have been saved
• Session info included in the scripts
• Cross-reference the working draft of the paper
• Confirm the code performs the intended analysis
• Confirm the code reproduces the reported results

Setup

Reproduce results

Verification

[github-actions]

🦙 MegaLinter status: ⚠️ WARNING

Descriptor	Linter	Files	Fixed	Errors	Warnings	Elapsed time
⚠️ BASH	bash-exec	32		28	0	0.12s
✅ BASH	shellcheck	32		0	0	0.27s
⚠️ BASH	shfmt	32		24	0	0.02s
⚠️ MARKDOWN	markdownlint	2		8	0	0.75s
✅ MARKDOWN	markdown-link-check	2		0	0	4.26s
✅ MARKDOWN	markdown-table-formatter	2		0	0	0.35s
✅ PYTHON	bandit	1		0	0	1.23s
✅ PYTHON	black	1		0	0	0.9s
✅ PYTHON	flake8	1		0	0	0.58s
⚠️ PYTHON	isort	1		1	0	0.26s
✅ PYTHON	mypy	1		0	0	8.65s
✅ PYTHON	pylint	1		0	0	3.62s
✅ PYTHON	pyright	1		0	0	2.71s
✅ PYTHON	ruff	1		0	0	0.03s
✅ R	lintr	15		0	0	12.5s

See detailed report in MegaLinter reports

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[tsoelter]

Looks great!! 🎉

[sashataluri]

Looks great! I just left some minor feedback.