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AlexsLemonade
/
scpca-downstream-analyses
This repository is intended to store our pipeline for marker genes analysis.
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Re-structure running the workflow docs
#328
cbethell
closed
1 year ago
2
Sync file path instructions
#327
cbethell
closed
1 year ago
1
Add documentation on working with ScPCA portal data
#326
cbethell
closed
1 year ago
2
Add theme and updated labels to GOI plots
#325
allyhawkins
closed
1 year ago
2
Separate `results_dir` from input dir variable in clustering and GOI modules
#324
cbethell
closed
1 year ago
1
Separate input data directory from results directory variable in clustering and GOI modules
#323
cbethell
closed
1 year ago
1
Move to conda-managed R
#322
jashapiro
closed
1 year ago
0
Remove outdated GOI files
#321
cbethell
closed
1 year ago
0
Rename Sections 2 and 3 in README
#320
dvenprasad
closed
1 year ago
1
Restructure running the workflow section in README
#319
dvenprasad
closed
1 year ago
1
Update normalization and variable genes metadata
#318
cbethell
closed
1 year ago
0
Update miQC filtering - remove cells with low gene count
#317
cbethell
closed
1 year ago
2
Use conda (mostly) to handle R dependencies
#316
jashapiro
closed
1 year ago
17
Prepare for scpca-downstream-analyses release v0.1.5
#315
cbethell
closed
1 year ago
0
Create an eval branch
#314
cbethell
closed
1 year ago
2
Add information to documentation on how to run modules using data from ScPCA
#313
allyhawkins
closed
1 year ago
2
Test clustering and GOI workflow with processed SCE objects from ScPCA
#312
allyhawkins
closed
1 year ago
1
Remove extra GOI files
#311
allyhawkins
closed
1 year ago
1
Change how variable genes are stored
#310
allyhawkins
closed
1 year ago
1
Change metadata for normalization
#309
allyhawkins
closed
1 year ago
1
Update miQC filtering to also remove cells with low gene count
#308
allyhawkins
closed
1 year ago
1
Make gene filtering optional in core workflow
#307
cbethell
closed
1 year ago
1
Use conda only(mostly) to handle R dependencies
#306
jashapiro
closed
1 year ago
3
Add note on what Snakemake is
#305
cbethell
closed
1 year ago
1
Sync processed SCE object file name
#304
cbethell
closed
1 year ago
1
Make gene filtering optional in core workflow
#303
allyhawkins
closed
1 year ago
1
Add note on what Snakemake is/how we use it to main README
#302
cbethell
closed
1 year ago
1
Sync fixing broken links to development
#301
allyhawkins
closed
1 year ago
0
Potential Conda/renv
#300
jashapiro
closed
1 year ago
4
Thought: Convert from renv to conda-native R package handling
#299
jashapiro
closed
1 year ago
1
Update processed SCE object file name
#298
cbethell
closed
1 year ago
1
Sync GOI example results files to S3
#297
cbethell
closed
1 year ago
0
Fix broken links and update release checklist
#296
allyhawkins
closed
1 year ago
1
Re-organize clustering module README and add section on colData contents
#295
cbethell
closed
1 year ago
1
Reorganize clustering module docs to mirror GOI module docs
#294
cbethell
closed
1 year ago
1
Sync clustering analysis results files to S3
#293
cbethell
closed
1 year ago
0
Sync core analysis results files to S3
#292
cbethell
closed
1 year ago
2
Sync ScPCA products
#291
allyhawkins
closed
1 year ago
1
Sync GOI example results to S3 and make link readily available
#290
cbethell
closed
1 year ago
1
Sync clustering example results to S3 and make link readily available
#289
cbethell
closed
1 year ago
1
Scpca-downstream-analyses Release v0.1.4
#288
cbethell
closed
1 year ago
0
Fix typo in link to docs
#287
cbethell
closed
1 year ago
0
Update GOI docs TOC
#286
cbethell
closed
1 year ago
0
Add overwrite option to GOI script
#285
cbethell
closed
1 year ago
1
Add section to GOI docs with details on mapping genes
#284
cbethell
closed
1 year ago
4
Prepare for scpca-downstream-analyses release v0.1.4
#283
cbethell
closed
1 year ago
1
Add overwrite option to GOI workflow
#282
cbethell
closed
1 year ago
1
Update GOI docs on how to run the workflow
#281
cbethell
closed
1 year ago
3
Initiate GOI Snakefile - Generate report rule
#280
cbethell
closed
1 year ago
0
Initiate GOI Snakefile - Calculations Rule
#279
cbethell
closed
1 year ago
1
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