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BodenmillerGroup
/
imcRtools
An R package for handling and analysing imaging mass cytometry data
https://bodenmillergroup.github.io/imcRtools/
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patchDetection fucntion with area output or patch area calculation
#80
SchulzDan
closed
2 years ago
5
Customized panel_file is not read correctly with read_steinbock()
#79
LazDaria
closed
2 years ago
1
Spatial context functions
#78
lassedochreden
closed
2 years ago
1
Fixed plotSpatial function
#77
nilseling
closed
2 years ago
0
Adjust edge detection approach
#76
nilseling
opened
2 years ago
0
Bug fix: specify number of nodes in patchDetection
#75
nilseling
closed
2 years ago
1
Fixed int_metadata duplication
#74
nilseling
closed
2 years ago
1
Bug fix: avoid duplication of metadata entries
#73
nilseling
closed
2 years ago
1
duplicated metadata entries
#72
nilseling
closed
2 years ago
3
KNN - "k must be positive"
#71
lassedochreden
closed
1 year ago
3
Bug fix: relevel group_by factors
#70
nilseling
closed
2 years ago
0
Re-level factor when calling testInteractions
#69
nilseling
closed
2 years ago
0
Patch detection fix
#68
nilseling
closed
2 years ago
0
Error when running patchDetection on a SpatialExperiment
#67
michaeljpitcher
closed
2 years ago
9
Updated for newest imc segmentation pipeline
#66
nilseling
closed
2 years ago
0
Read last entry of metal isotope from file
#65
nilseling
closed
2 years ago
0
Cannot readSCEfromTXT
#64
l2baeriswyl
closed
2 years ago
11
readSCEfromTXT
#63
sailseem
closed
2 years ago
5
clustered_neighbors
#62
sailseem
closed
2 years ago
2
Change regex of readSCEformTXT function
#61
nilseling
closed
2 years ago
4
Initialize objects with colnames
#60
nilseling
closed
11 months ago
1
Select files more specifically
#59
nilseling
closed
2 years ago
0
Fixed indexing issue with steinbock graphs
#58
nilseling
closed
2 years ago
0
Error in .steinbock_read_graphs function
#57
nilseling
closed
2 years ago
3
Read txt fix
#56
nilseling
closed
2 years ago
0
Delaunay
#55
nilseling
closed
2 years ago
0
Compute proximity metrics
#54
nilseling
opened
2 years ago
0
NeighbouRhood files
#53
aleixriusr
closed
2 years ago
3
Classic bug fix
#52
nilseling
closed
2 years ago
1
Adjust count for classic and patch testInteraction function
#51
nilseling
closed
2 years ago
1
Figure out if the testInteraction produces symmetric results
#50
nilseling
closed
1 year ago
1
Restructure
#49
nilseling
closed
3 years ago
1
return output of the permutation tests
#48
Rcasan
closed
1 year ago
2
Bug fix
#47
nilseling
closed
3 years ago
1
testInteractions() error
#46
erikgerdtsson
closed
1 year ago
7
Add max distance thresholding to Delaunay triangulation
#45
nilseling
closed
2 years ago
1
Move all helper functions into a single script
#44
nilseling
closed
3 years ago
1
Rewrite testInteractions function to increase speed
#43
nilseling
opened
3 years ago
1
Expand unit tests and validity checks
#42
nilseling
closed
1 year ago
4
Added supervised patch detection function
#41
nilseling
closed
3 years ago
0
Add verbose parameter to testInteractions
#40
nilseling
closed
3 years ago
1
Check that centroid-0 and centroid-1 fit to X and Y axis
#39
nilseling
closed
3 years ago
2
Read steinbock metadata from images.csv
#38
jwindhager
closed
3 years ago
5
Bioc cleanup
#37
nilseling
closed
3 years ago
0
Bioc cleanup
#36
nilseling
closed
3 years ago
0
Bioc cleanup
#35
nilseling
closed
3 years ago
0
Bioc cleanup
#34
nilseling
closed
3 years ago
0
First PR for Bioconductor submission
#33
nilseling
closed
3 years ago
1
Change in steinbock graph file format
#32
jwindhager
closed
3 years ago
4
General fixes to address open issues
#31
nilseling
closed
3 years ago
1
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