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sc-data-integration
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Evaluate CellAssign metrics
#231
allyhawkins
closed
1 year ago
5
Explore copyKat performance on RMS data
#230
sjspielman
closed
1 year ago
8
Compare CellAssign annotations using custom marker gene sets from PanglaoDB
#229
allyhawkins
closed
1 year ago
2
Compare cell type annotations for RMS samples to SingleR annotations
#228
allyhawkins
closed
1 year ago
2
Minor updates to rendering SingleR report
#227
allyhawkins
closed
1 year ago
0
Identify a similar metric to the median delta for CellAssign
#226
allyhawkins
closed
1 year ago
0
Evaluate combining marker gene lists from multiple organs with PanglaoDb
#225
allyhawkins
closed
1 year ago
0
Rerun SingleR analysis with RMS libraries
#224
allyhawkins
closed
1 year ago
0
Use marker genes from defined cell types as reference for CellAssign
#223
allyhawkins
closed
1 year ago
1
Identify a CNV inference method to use for annotating tumor and normal cells
#222
jashapiro
opened
1 year ago
13
Test Cell Assign against known cell types in sarcoma
#221
allyhawkins
closed
1 year ago
4
Future thought: Explore disagreements between references
#220
allyhawkins
opened
1 year ago
0
Combine immune references for SingleR
#219
allyhawkins
closed
1 year ago
3
Try CellAssign on a different tissue type
#218
allyhawkins
closed
1 year ago
0
Test SingleR with combining immune references
#217
allyhawkins
closed
1 year ago
0
Render SingleR analysis reports for multiple libraries
#216
allyhawkins
closed
1 year ago
0
Explore marker genes based cell type assignment methods
#215
allyhawkins
closed
1 year ago
1
Evaluate metrics for SingleR on multiple libraries
#214
allyhawkins
closed
1 year ago
0
Test marker genes cell type annotation method
#213
allyhawkins
closed
1 year ago
0
Consider removing occurrences of `aes_string()`
#212
sjspielman
opened
1 year ago
1
Plot within batch ARI
#211
allyhawkins
closed
1 year ago
2
Dive into SingleR and comparing references with and without immune cells
#210
allyhawkins
closed
1 year ago
5
Remove immune and immune-related cell types from celldex refs for cell typing
#209
allyhawkins
closed
1 year ago
1
Permute celldex ref labels and compare true cell assignment to distribution of assignments
#208
allyhawkins
opened
1 year ago
1
Create non-immune cell type refs from HPCA celldex ref
#207
allyhawkins
closed
1 year ago
0
Add function for calculating reverse ARI
#206
allyhawkins
closed
1 year ago
5
Add parameter for merge order and integration order
#205
allyhawkins
closed
1 year ago
1
Setup exploration of cell type annotation added to `scpca-nf` with Gawad project
#204
allyhawkins
closed
1 year ago
1
Add a plot for reverse ARI and test with simulated data
#203
allyhawkins
closed
1 year ago
0
Function for comparing pre correction clustering to post correction clustering
#202
allyhawkins
closed
1 year ago
0
Add parameter for specifying merge order and test with integrated ScPCA data
#201
allyhawkins
closed
1 year ago
0
Clean up scpca metadata files and readme
#200
allyhawkins
closed
1 year ago
0
Fix typo in error message
#199
jaclyn-taroni
closed
1 year ago
0
seurat integration investigation
#198
sjspielman
opened
1 year ago
1
Bump Seurat to 4.2
#197
sjspielman
opened
1 year ago
0
Cell type annotation exploratory notebook
#196
sjspielman
closed
1 year ago
7
Remove old sce_dir and similar
#195
sjspielman
closed
1 year ago
0
Discussion: Plan for moving data integration to `scpca-nf`
#194
allyhawkins
closed
1 year ago
1
Add stacked barplots and legend label counts
#193
sjspielman
closed
1 year ago
1
Report fixes
#192
sjspielman
closed
1 year ago
1
Prep for Gawad data
#191
sjspielman
closed
1 year ago
0
Add cell type numbers to plot legends
#190
allyhawkins
closed
1 year ago
0
Visualize relationship between batches and cell types
#189
allyhawkins
closed
1 year ago
1
Check UMAP plot colors
#188
sjspielman
closed
1 year ago
0
Fix analysis report cLISI text
#187
sjspielman
closed
1 year ago
0
Remove mention of sce directory present in metadata files
#186
allyhawkins
closed
1 year ago
1
Script to process CITEseq
#185
sjspielman
closed
1 year ago
0
Script to normalize CITE-Seq data
#184
sjspielman
closed
1 year ago
12
Integrate RMS data and add param for choosing projects to integrate
#183
allyhawkins
closed
1 year ago
9
Add `asw_separate_celltypes` param
#182
sjspielman
closed
1 year ago
3
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