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BodenmillerGroup
/
IMCDataAnalysis
R based workflow for multiplexed imaging data
https://bodenmillergroup.github.io/IMCDataAnalysis/
MIT License
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Running stats on marker expression between groups
#103
rebekahdadey
opened
1 month ago
0
Phenograph Clustering
#102
tbudiman7
closed
3 months ago
1
Marker disappeared in the heatmap
#100
giuliospinozzi
closed
5 months ago
4
Data availability
#99
jcasadogp
closed
5 months ago
1
Using IMCDataAnalysis with HistoCAT-exported Data
#98
sbeber16
closed
5 months ago
1
train-classifier
#97
SimonSichone
closed
5 months ago
3
Updated plotCells object scaling
#96
lassedochreden
opened
7 months ago
0
no detected spatial_community, empty heatmap
#95
Elena983
closed
6 months ago
7
Problem with confusion matrix
#94
RiccardoSin
closed
7 months ago
3
Problem with concatenation
#93
GiCarlu
closed
7 months ago
2
Read in and consolidate labeled data(remove-doublets)phenotyping section.
#91
SimonSichone
closed
7 months ago
4
Subset the SPE object for cell-level visualization
#90
nilseling
opened
7 months ago
0
Analysis workflow for IMC data after segmentation in HALO
#92
alexeykb
closed
3 months ago
2
8.3 Seurat correction - problems
#89
GiCarlu
closed
7 months ago
3
packages dosen't contain needed functions
#88
GiCarlu
closed
8 months ago
2
cytoviewer citation update
#87
lassedochreden
closed
8 months ago
2
Update DEVELOPMENT.md
#86
nilseling
closed
9 months ago
0
Devel
#85
nilseling
closed
9 months ago
0
Also visualize the CN heatmap without column scaling
#84
nilseling
closed
9 months ago
1
Question about batch effect correction
#83
EmilyZou123
closed
9 months ago
7
Normalize is defunct
#82
tryggest
closed
11 months ago
1
Number of cell for each sample
#81
giuliospinozzi
closed
12 months ago
1
Same sample colors between different heatmaps
#80
giuliospinozzi
closed
12 months ago
1
Subclustering of PhenoGraph clusters
#79
marleneweiss
closed
1 year ago
12
12.1 Spatial Interaction Graphs: No graph, only title
#78
Will760
closed
1 year ago
2
11.2.1 Visualizing metadata: Error in .valid.colour(...)
#77
Will760
closed
1 year ago
2
10.4.1 Publication-ready ComplexHeatmap not generating anything but no errors
#76
Will760
closed
1 year ago
4
silhouette width score (Cell Phenotyping)
#75
wqcho00
closed
1 year ago
2
Fast MNN batch correction: more singular values/vectors requested than available
#74
Will760
closed
1 year ago
2
Process a single ROI
#73
giuliospinozzi
closed
1 year ago
1
PlotPixels: Segmentation masks must only contain integer values
#72
giuliospinozzi
closed
1 year ago
4
How to exclude an image from analysis if cell density is too low.
#71
Will760
closed
1 year ago
3
Tests to setup Docker on macOS runner
#70
nilseling
closed
1 year ago
0
Devel
#69
nilseling
closed
1 year ago
0
Set the seed for clustering
#68
nilseling
closed
1 year ago
0
Add more information how to set the seed in detectCommunities
#67
nilseling
closed
1 year ago
1
Unusually low marker expression?
#66
Yanira1208
closed
1 year ago
2
spillover correction
#65
rahilgholami
closed
1 year ago
10
Updates for resubmission
#64
nilseling
closed
1 year ago
0
Add cytoviewer to workflow
#63
lassedochreden
closed
1 year ago
1
Construction of spatial graphs for neighbourhood analysis
#62
zoqaiyum
closed
1 year ago
3
Any idea why the last error occurs?
#60
StiThor
closed
1 year ago
7
Error when performing fastMNN batch correction
#61
marleneweiss
closed
1 year ago
2
Imaging mass cytometry data analysis
#59
StiThor
closed
1 year ago
14
Fixes to pass checks
#58
nilseling
closed
1 year ago
0
One of my gated cells is missing (9.3 Classification Approach)
#57
zoqaiyum
closed
1 year ago
1
Run normalize with only 1 sample
#56
rebekahdadey
closed
1 year ago
3
Transformation of IMC data
#55
zoqaiyum
closed
1 year ago
7
Rphenograph clustering codes not working
#54
zoqaiyum
closed
1 year ago
1
Recompiled final workflow
#53
nilseling
closed
1 year ago
0
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