feat: new SINCLAIR functions

[wong-nw]

Changes

Primary upload to include SINCLAIR functions:

• seurat_clustering
• convert_to_human_genelist
• main_process_so -> seurat_preprocess
• run_singleR
• main_singleR -> run_SingleR_db
• main_doublets -> filter_doublets
• run_singleR_average -> run_SingleR_cluster
• main_batch_correction -> run_batch_correction

Includes ad hoc functions which will also be updated as needed for formatting:

• bubble_plot
• calc_sc_gsea_score
• cluster_metrics
• convert_mtx_to_h5
• run_hypergeometric_test
• splitFeaturePlot
• volcano_plot

Issues

Resolves #6 by migrating the substance of https://github.com/CCBR/SINCLAIR/blob/main/bin/scRNA_functions.R into an R package.

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• Write unit tests for any new features, bug fixes, or other code changes.
• Update the docs if there are any API changes (roxygen2 comments, vignettes, readme, etc.).
• [ ] Update NEWS.md with a short description of any user-facing changes and reference the PR number. Follow the style described in https://style.tidyverse.org/news.html
• Run devtools::check() locally and fix all notes, warnings, and errors.

[kelly-sovacool]

There are remnants from unsolved merge conflicts in a few files, please remove them

They look like this:
<<<<<<< HEAD
=======
>>>>>>> COMMIT_HASH

[kelly-sovacool]

Now would be a great time to create or borrow a very small test dataset and create unit tests -- see https://usethis.r-lib.org/reference/use_r.html

[kelly-sovacool]

All of the comments I left previously haven't been addressed. Please either commit the suggestion, push a commit that addresses the comment, or respond to the comment to start a discussion about the merits of the suggestion. Only mark the conversation as resolved once it has either been addressed or we've discussed that it doesn't need to be addressed.

[kelly-sovacool]

Also, please run pre-commit install in your local clone of this repo

[wong-nw]

Also, please run pre-commit install in your local clone of this repo

Done

[kelly-sovacool]

R CMD check failed -- I'll work on fixing the problems and push to this branch directly. Later we can have a debrief about it so you can pre-empt these problems as you write code.
https://github.com/CCBR/SCOT/actions/runs/17109318156/job/48526459850?pr=7#step:6:201

[kelly-sovacool]

notes from devtools::check() that I'm fixing:

❯ checking dependencies in R code ... NOTE
  Namespaces in Imports field not imported from:
    ‘SingleCellExperiment’ ‘grDevices’ ‘ontologyIndex’ ‘utils’
    All declared Imports should be used.

❯ checking R code for possible problems ... [36s/50s] NOTE
  make_bubble_plot: warning in AverageExpression(so, assay = assay):
    partial argument match of 'assay' to 'assays'
  run_AUCell: warning in AUCell_exploreThresholds(cells_AUC, plotHist =
    FALSE, assign = TRUE): partial argument match of 'assign' to
    'assignCells'
  convert_human_gene_list: no visible binding for global variable ‘gns’
  make_bubble_plot: no visible binding for global variable ‘pct.exp’
  make_bubble_plot: no visible binding for global variable ‘id’
  make_bubble_plot: no visible binding for global variable
    ‘features.plot’
  make_bubble_plot: no visible global function definition for ‘melt’
  make_bubble_plot: no visible binding for global variable ‘group’
  make_bubble_plot: no visible binding for global variable ‘Gene’
  make_bubble_plot: no visible binding for global variable ‘Pct.Exp’
  make_bubble_plot: no visible binding for global variable ‘AvgExp’
  preprocess_sample: no visible binding for global variable ‘cc.genes’
  run_batch_correction: no visible binding for global variable
    ‘scVIIntegration’
  run_batch_correction: no visible global function definition for
    ‘RunOptimizeALS’
  run_batch_correction: no visible global function definition for
    ‘RunQuantileNorm’
  run_batch_correction: no visible binding for global variable ‘v_list’
  run_singleR_cluster: no visible binding for global variable ‘refFile’
  split_featurePlot: no visible global function definition for
    ‘DefaultDimReduc’
  split_featurePlot: no visible global function definition for ‘dev.new’
  Undefined global functions or variables:
    AvgExp DefaultDimReduc Gene Pct.Exp RunOptimizeALS RunQuantileNorm
    cc.genes dev.new features.plot gns group id melt pct.exp refFile
    scVIIntegration v_list
  Consider adding
    importFrom("grDevices", "dev.new")
  to your NAMESPACE file.

[kelly-sovacool]

Down to 2 remaining R CMD check notes:

── R CMD check results ──────────────────────────────────────────────────────────────────────────────────────────────────────────────── SCOT 0.0.0.9000 ────
Duration: 4m 28.7s

❯ checking package dependencies ... NOTE
  Imports includes 24 non-default packages.
  Importing from so many packages makes the package vulnerable to any of
  them becoming unavailable.  Move as many as possible to Suggests and
  use conditionally.

❯ checking R code for possible problems ... [30s/44s] NOTE
  preprocess_sample: no visible binding for global variable ‘cc.genes’
  run_singleR_cluster: no visible binding for global variable ‘refFile’
  Undefined global functions or variables:
    cc.genes refFile

0 errors ✔ | 0 warnings ✔ | 2 notes ✖

• We can ignore the one about package dependencies unless we submit this to CRAN. Let's kick that can down the road until we cross that bridge.
• The global variable notes are genuine problems that need to be fixed, otherwise those functions will not work. I'll open a separate issue so we can merge this PR.