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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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Need to `as.matrix()` before `BiocNeighbors::findKNN()`
#127
LTLA
opened
1 day ago
0
Feature request: extend the aggregateNeighbors functionality
#126
nilseling
opened
1 month ago
0
replace minDistToCells by distToCells
#125
brunopalau
opened
2 months ago
2
Memory Issue with minDistToCells
#124
jonhsussman
opened
5 months ago
1
Select neighbours
#123
aleixrius
closed
7 months ago
2
Add an additional check that spot_ids in binAcrossPixels match before aggregation
#122
nilseling
closed
8 months ago
1
Plot spatial aes fix
#121
nilseling
closed
9 months ago
1
Avoid initializing spatialCoords with rownames
#120
nilseling
closed
10 months ago
0
Test interaction test
#119
nilseling
closed
10 months ago
1
Feature: Add option to testInteractions which removes unconnected cells before testing significance
#118
nilseling
closed
10 months ago
1
Bug notice: testInteractions p-values are not perfectly exact calculated
#117
nilseling
closed
10 months ago
1
Update example data
#116
nilseling
closed
11 months ago
1
Changes to read_steinbock validity checking, see NEWS
#115
nilseling
closed
12 months ago
1
Update test data to newest version
#114
nilseling
closed
11 months ago
1
Bug fix: set ratio between physical units correctly in plotSpatial
#112
nilseling
closed
1 year ago
1
Fix `aspect.ratio` argument in `plotSpatial`
#111
nilseling
closed
12 months ago
1
Error when trying to perform spillover correction on spe
#110
marleneweiss
closed
1 year ago
12
testInteractions docs
#109
nilseling
closed
1 year ago
1
Adjustments to detectCommunity docs
#108
nilseling
closed
1 year ago
0
Error when executing read_steinbock command
#106
marleneweiss
closed
1 year ago
6
Test interaction fix
#105
nilseling
closed
1 year ago
0
Bug fix: patchDetection function does not perform correctly if cells are not grouped by image
#104
nilseling
closed
1 year ago
1
Bug fix: label permutation reorders cells
#103
nilseling
closed
1 year ago
1
What are FirstLabel, SecondLabel, ct in dat_baseline meaning?
#102
ZeroLi-Bio
closed
1 year ago
2
aggregateNeighbors produces NA
#101
roskcl
closed
1 year ago
1
Adjust `aes_` to `aes(.data[[]])`
#100
nilseling
closed
8 months ago
1
added option to return permutation samples
#99
nilseling
closed
1 year ago
0
Replace merge by left_join
#98
nilseling
closed
1 year ago
1
Fixed bug with .calc_p_vals util function
#97
ajxa
closed
1 year ago
7
Adjust the wat parallelisation is used
#96
nilseling
opened
1 year ago
0
"Minimal spanning tree" function
#95
lassedochreden
opened
1 year ago
0
read_steinbock for multiple folders
#93
paulrbuckley-kcl
closed
1 year ago
3
Error when loading imcRtool library
#92
tryggest
closed
1 year ago
2
minDistToCells - Error
#91
StefanosVoglis
closed
1 year ago
4
Axis ratio
#90
nilseling
closed
1 year ago
0
Exclude validity check until next release
#89
nilseling
closed
1 year ago
0
Error when using DittoSeq/Heatmap plots
#88
jweis3
closed
1 year ago
2
Community detection function
#87
lassedochreden
closed
1 year ago
2
Suggest to fix aspect ratio by default
#86
shazanfar
closed
1 year ago
2
Rotate images from .txt IMC file
#85
AlessiaCaramello
closed
2 years ago
7
Add function for spatial community detection
#84
lassedochreden
closed
1 year ago
3
Distance to patch
#83
SchulzDan
closed
2 years ago
2
Fix `ncols` and `nrows` argument in `plotSpatial`
#82
nilseling
closed
2 years ago
1
Patch detection update
#81
nilseling
closed
2 years ago
1
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
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