ScPCA Downstream Analyses v0.1.6

What's Changed

• Addition of data integration module
• Update independent installation docs

Full Changelog: v0.1.5...v0.1.6

ScPCA Downstream Analyses v0.1.5

What's Changed

• Sync core analysis results files to S3 in #292
• Sync clustering analysis results files to S3 in #293
• Fix broken links and update release checklist in #296
• Re-organize clustering module README and add section on colData contents in #295
• Sync GOI example results files to S3 in #297
• Sync processed SCE object file name in #304
• Add note on what Snakemake is in #305
• Make gene filtering optional in core workflow in #307
• Update miQC filtering - remove cells with low gene count in #317
• Update normalization and variable genes metadata in #318
• Remove outdated GOI files in #321
• Move to conda-managed R in #322
• Separate results_dir from input dir variable in clustering and GOI modules in #324
• Add documentation on working with ScPCA portal data in #326
• Sync file path instructions in #329
• Re-structure running the workflow docs in #328
• Set theme and update GOI plot labels in #330

Full Changelog: v0.1.4...v0.1.5

Usability Eval Release

This release should be used to conduct usability evals of the core downstream analysis workflow.

ScPCA Downstream analysis v0.1.4 - Genes of Interest Module Refactor

This release refactors the optional genes of interest (GOI) module to help users better evaluate expression of a specific list of genes in a sample dataset.

What's Changed

• Move independent installation instructions to separate doc in #248
• Add GOI analysis calculations script in #230
• Replace expected output screenshot with code block in #251
• Add more details on the mitochondrial gene list in #252
• Make link to processing info doc more prominent in #254
• Move filtering method to config file in #255
• Add QuickStart guide to README in #256
• Add section on core workflow output SCE contents in #257
• Document core analysis template report in #261
• Update development w/ core changes merged into main in #264
• Initiate GOI module README in #246
• Refactor GOI template notebook in #232
• Add number of filtered cells to metadata of SCE in #269
• Add UMAP plot labels in core workflow in #268
• Fix how we handle annotation when gene set is NULL in #271
• Generalize GOI plotting functions in #270
• Add example results files to repo/Ignore project-specific files in #276
• Update core analysis docs in #278
• Initiate GOI Snakefile - Calculations Rule in #279
• Initiate GOI Snakefile - Generate report rule in #280
• Add overwrite option to GOI script in #285
• Update GOI docs on how to run the workflow in #281
• Add section to GOI docs with details on mapping genes in #284
• Update GOI docs TOC by in #286
• ScPCA-downstream-analyses Release v0.1.4 in #288

Full Changelog: v0.1.3...v0.1.4

ScPCA Downstream analysis v0.1.3 - Core Workflow Updates

This release includes documentation and structural updates to the core workflow analysis.

What's Changed

• Move independent installation instructions to a separate doc in #248
• Replace expected output screenshot with code block in #251
• Add more details on the mitochondrial gene list in #252
• Move filtering method to config file and metadata file to example-data in #255
• Add quick start guide section to README in #256
• Add subsection on SCE contents in #257
• Document core analysis report template in #261

Full Changelog: v0.1.2...v0.1.3

ScPCA Downstream Analyses v0.1.2 - Addition of the Clustering Module

This release includes the addition of the optional clustering module which can be used to explore different methods of clustering and test a range of parameter values for given graph-based clustering methods in order to identify the optimal clustering for each library.

What's Changed

• Update R to 4.2 & Bioconductor to 3.15 in #202
• Add optional clustering calculations script in #191
• Add overwrite option to optional clustering calculations script in #203
• Add docs to clustering template notebook in #210
• Add optional clustering report template in #207
• Initialize optional clustering directory README in #213
• Fix restore argument to use input lockfile in #216
• Pin pandoc version in #219
• Initiate Snakefile for optional clustering module - calculations rule in #214
• Optional clustering Snakefile - rendering template report rule in #215
• How to run the optional clustering workflow docs in #220
• Add logs to snakemake rules in #222
• Implement docs feedback from heuristic walkthrough in #223
• Account for additional cluster_type in clustering calculations script in #224
• Account for additional cluster_type in clustering report in #226
• Fix typos in README.md in #234

Full Changelog: v0.1.1...v0.1.2

ScPCA Downstream analysis v0.1.1

Fixes workflow path error

What's Changed

• fix extra slash in #204

Full Changelog: v0.1.0...v0.1.1

Initial Release of ScPCA Downstream Analyses Workflow v0.1.0

This is the initial release of the core workflow in scpca-downstream-analyses used for analyzing single-cell gene expression data available on the Single-cell Pediatric Cancer Atlas Portal. The workflow performs filtering, normalization, dimensionality reduction, and clustering of individual single-cell libraries, returning the processed single-cell data and a summary report for each library.