bimberlabinternal CellMembrane issues

bimberlabinternal / CellMembrane

An R package with wrappers and pipelines for single cell RNA-seq analysis

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issues

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Bugfix to GetMsigdbGeneSet

#265 bbimber closed 2 days ago
0
Add ClusteredDotPlot

#264 GWMcElfresh closed 1 month ago
1
ADT Triage and Classification

#263 GWMcElfresh opened 1 month ago
1
Support for alphanumeric groupFields in TCR diversity calculation

#262 GWMcElfresh closed 1 month ago
0
scTour: avoid 'SparseCSRView' object has no attribute 'A' error.

#261 bbimber closed 1 month ago
7
Pairwise find markers

#260 bbimber closed 2 months ago
0
Make tSNE optional

#259 bbimber closed 3 months ago
0
add alternative ssGSEA

#258 GWMcElfresh opened 3 months ago
1
nCountRNAStratification within PseudobulkSeurat has matrix vs vector related issues

#257 GWMcElfresh opened 3 months ago
0
use more factor-friendly equivalance check in RunFilteredContrasts

#256 GWMcElfresh closed 3 months ago
0
More rigorous check for which layers to join

#255 bbimber closed 3 months ago
0
Use ScaleData for escape

#254 bbimber closed 3 months ago
0
Improve error handling around no DEGs in bar plot

#253 GWMcElfresh closed 3 months ago
0
Bugfix to MergeSeurat with split layers and multiple assays

#252 bbimber closed 3 months ago
0
PseudobulkingBarPlot may want to check if there are any statistically significant DEGs

#251 daramirez opened 3 months ago
3
fixes bug in creation of pcts matrix

#250 gboggy2 closed 3 months ago
1
Normalize ssGSEA data based on library size

#249 bbimber closed 3 months ago
0
PseudobulkingDEHeatmap with geneSpace with 1 gene only

#248 daramirez opened 3 months ago
0
Drop scMetabolism, due to install failure on VISION, due to loe being…

#247 bbimber closed 3 months ago
0
Fix to pseudobulk when a given group only has one cell

#246 bbimber closed 3 months ago
0
pct.expression should store a percent not number of cells

#245 bbimber closed 4 months ago
1
Try to fix test failure on Bioc 3.18

#244 bbimber closed 4 months ago
0
Adding percentage assay

#243 daramirez closed 4 months ago
2
Asymmetric LogCPM measurements in the list-of-contrasts returned from `RunFilteredContrasts()` & Percent expression inclusion in the pseudobulked seurat object.

#242 GWMcElfresh closed 4 months ago
2
`PseudobulkingDEHeatmap` needs additional sanity checks on the input. Values of `contrastField` with spaces (and hyphens?) sometimes cause the entries of `RunFilteredContrasts()`'s list of dataframes to be lists, instead of individual strings/floats. Very likely to be a missing `make.names()` call or gsub somewhere.

#241 GWMcElfresh closed 4 months ago
0
Bug fix related to non-alphanumeric characters in pseudobulking pipelines

#240 GWMcElfresh closed 4 months ago
1
CalculateClusterEnrichment

#239 GWMcElfresh closed 4 months ago
3
Improvements to Pseudobulking Pipelines

#238 GWMcElfresh opened 4 months ago
0
PseudobulkingBarPlot improvements

#237 GWMcElfresh closed 4 months ago
6
fix warning in FilterPseudobulkContrasts()

#236 GWMcElfresh closed 5 months ago
0
Improve SingleR handling when some cells have zero counts on the selected genes

#235 bbimber closed 5 months ago
0
decrement escape version

#234 GWMcElfresh closed 5 months ago
0
Bugfixes to escape/dim redux

#233 bbimber closed 5 months ago
0
Add option to run PCA/UMAP on escape/ssGSEA data

#232 bbimber closed 5 months ago
0
Update Docker base image

#231 bbimber closed 6 months ago
0
Convert underscore to hyphen in GSEA gene set names

#230 bbimber closed 6 months ago
0
Improve detection of split layers

#229 bbimber closed 6 months ago
0
Pseudobulk analysis

#228 daramirez closed 5 months ago
7
Include assayName in escape/gsea

#227 bbimber closed 6 months ago
0
Debug seurat layer join after merge

#226 bbimber closed 6 months ago
0
Always join layers after seurat merge

#225 bbimber closed 6 months ago
0
add msigdb gene set parsing to RunEscape

#224 GWMcElfresh closed 6 months ago
4
Ensure underscore replaced with hyphen in PseudobulkSeurat

#223 bbimber closed 6 months ago
0
Drop assay of stored ranks prior to merge

#222 bbimber closed 6 months ago
0
Support escape and CS-CORE

#221 bbimber closed 6 months ago
0
Improve the UCell-based Cell Cycle function

#220 bbimber closed 6 months ago
0
Use release-specific install_bioc_sysdeps.sh

#219 bbimber closed 6 months ago
0
Add flag in CalculateUcellPerFeature to ignore existing cached ranks

#218 bbimber closed 6 months ago
0
Avoid warning in AppendCiteSeq

#217 bbimber closed 7 months ago
0
Update test to ensure scMetabolism is not in an assay

#216 bbimber closed 7 months ago
0