HelenaLC CATALYST issues

HelenaLC / CATALYST

Cytometry dATa anALYsis Tools

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issues

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Exporting raw expression values

#398 kmincham opened 4 days ago
0
visualising specific clusters using plotPbExprs

#397 satsumayo closed 1 week ago
1
plotMultiHeatmap-how to change the color

#396 TongzhenXu closed 2 weeks ago
0
panel[[panel_cols$channel]] %in% colnames(fs) are not all TRUE

#395 Behind42 opened 4 weeks ago
3
How to change condition bar color in the plotExprHeatmap function

#394 TongzhenXu closed 4 weeks ago
3
plotClusterHeatmap deprecated and now unable to extract the same data from the new Heatmap functions

#393 DrFedericaOrsenigo closed 1 month ago
1
MDS plot

#392 galvaresborges closed 2 weeks ago
2
Speeding up clustering & DR process

#391 fy711 closed 3 months ago
2
Import celltype annotations

#390 MDHowe4 closed 3 weeks ago
1
Convert Cell Proportions To Values

#389 ramziabb opened 4 months ago
2
plotAbundances Adjusts Stacked Bar Width According to Grouping

#388 LukaTandaric closed 4 months ago
3
Is rowData and colData switched in the clustering part of the differential vignette?

#387 Sandyna closed 1 week ago
2
Compensation

#386 PhillipSsekamatte closed 5 months ago
1
I cant't get all my features within sce

#385 PhillipSsekamatte closed 5 months ago
0
pbMDS Function Stopped Working

#384 LukaTandaric closed 4 months ago
4
plotDiffHeatmap sort by condition

#383 SamWell16 closed 6 months ago
4
plotDiffHeatmap: avoid failure when only one cluster remains

#382 SamGG closed 2 weeks ago
4
plotDiffHeatmap : ambiguity when multiple clusterings could match

#381 SamGG opened 6 months ago
2
Subset or filter out cells based on UMAP coordinates

#380 vmkalbskopf closed 6 months ago
3
How to identify/visualize co-expression (correlation) between markers?

#379 WilliamMWei closed 6 months ago
1
FlowSOM Clustering

#378 KStrange94 closed 4 months ago
5
More shapes than the 17 supported when connect paired samples with plotAbundances? #197

#377 M4artin closed 7 months ago
1
Installation of CATALYST not working

#376 AdrienSchv closed 8 months ago
4
library(CATALYST) Error

#375 yutingdai1125 closed 6 months ago
2
How to combine correctly SCE objects

#374 MargolinGaby closed 8 months ago
1
Combining several SCE elements into one

#373 MargolinGaby closed 8 months ago
5
Clustering by specific marker

#372 7DiM7 closed 6 months ago
1
How to increase the default colour scheme of CATALYST?

#371 zoqaiyum closed 8 months ago
2
densvis, scuttle, scatter cannot be installed

#370 Jeffchingg closed 9 months ago
3
Clarification about re-clustering/sub-clustering

#369 denvercal1234GitHub closed 9 months ago
3
Importing back csv files exported from sce object will not preserve the unique cell id read in CATALYST

#368 denvercal1234GitHub opened 10 months ago
0
How to use CATALYST::plotAbundances to plot cluster's abundance at certain metaclustering?

#367 denvercal1234GitHub closed 10 months ago
3
filterSCE() version 1.22.0

#366 83years opened 10 months ago
5
How to remove certain markers/channels after clustering with CATALYST::filterSCE?

#365 denvercal1234GitHub closed 10 months ago
1
Using HARMONY Batch-corrected data for downstream analysis on CATALYST

#364 satsumayo closed 10 months ago
1
Error in prepData(fs, panel, md, features = panel$fcs_colname) : all(unlist(md_cols) %in% names(md)) is not TRUE

#363 CalmRealistic closed 11 months ago
7
Named UMAPs

#362 purisuto closed 11 months ago
3
estCutoffs produces `Warning: NaNs produced`

#361 nilseling closed 11 months ago
1
`sce2fcs`: Error in if (any(idx)) { : missing value where TRUE/FALSE needed, and Warning channel_alias: Multiple channels from one FCS are matched to the same alias!

#360 denvercal1234GitHub closed 10 months ago
2
plotExprHeatmap function fails

#359 isimove closed 6 months ago
4
`CATALYST::plotPbExprs` produces none of the cells at 0 expression and reducedDims.UMAP have cells squeezed at 0?

#358 denvercal1234GitHub closed 11 months ago
4
Subset out of bounds issue

#357 LenHC closed 6 months ago
5
`prepData()` unexpectedly create "exprs" if doing manual transformation using FlowJo for FACS?

#356 denvercal1234GitHub closed 11 months ago
3
Clarification for arguments features and color_by in plotNRS()

#355 denvercal1234GitHub closed 1 year ago
3
Subset out of bounds when creating single cell experiment

#354 Tregwiz closed 6 months ago
2
Error in if (all(abs(as.numeric(labels_y) - as.numeric(y)) < 1e-04)) { : missing value where TRUE/FALSE needed

#353 denvercal1234GitHub closed 4 months ago
2
Clustering >15 million cells with CATALYST cluster

#352 dstueckm closed 1 year ago
1
Error in prepData

#351 FRLab closed 1 year ago
1
CATALYST::pbMDS produced plots with cluster cells clumped together on 1 side?

#350 denvercal1234GitHub closed 1 year ago
1
How to ensure non-marker parameters are not used for clustering analyses (prepData(FACS=F))?

#349 denvercal1234GitHub closed 1 year ago
2