BodenmillerGroup/imcRtools issues and pull requests

#125 - replace minDistToCells by distToCells

Pull Request - State: open - Opened by brunopalau 13 days ago - 2 comments

#101 - aggregateNeighbors produces NA

Issue - State: closed - Opened by roskcl about 1 year ago - 1 comment

#100 - Adjust `aes_` to `aes(.data[[]])`

Issue - State: closed - Opened by nilseling about 1 year ago - 1 comment

#99 - added option to return permutation samples

Pull Request - State: closed - Opened by nilseling over 1 year ago

#98 - Replace merge by left_join

Pull Request - State: closed - Opened by nilseling over 1 year ago - 1 comment

#97 - Fixed bug with .calc_p_vals util function

Pull Request - State: closed - Opened by ajxa over 1 year ago - 7 comments

#96 - Adjust the wat parallelisation is used

Issue - State: open - Opened by nilseling over 1 year ago

#95 - "Minimal spanning tree" function

Issue - State: open - Opened by lassedochreden over 1 year ago

#93 - read_steinbock for multiple folders

Issue - State: closed - Opened by paulrbuckley-kcl over 1 year ago - 3 comments

#92 - Error when loading imcRtool library

Issue - State: closed - Opened by tryggest over 1 year ago - 2 comments

#91 - minDistToCells - Error

Issue - State: closed - Opened by StefanosVoglis over 1 year ago - 4 comments

#90 - Axis ratio

Pull Request - State: closed - Opened by nilseling over 1 year ago

#89 - Exclude validity check until next release

Pull Request - State: closed - Opened by nilseling over 1 year ago

#88 - Error when using DittoSeq/Heatmap plots

Issue - State: closed - Opened by jweis3 almost 2 years ago - 2 comments

#87 - Community detection function

Pull Request - State: closed - Opened by lassedochreden almost 2 years ago - 2 comments

#86 - Suggest to fix aspect ratio by default

Issue - State: closed - Opened by shazanfar almost 2 years ago - 2 comments

#85 - Rotate images from .txt IMC file

Issue - State: closed - Opened by AlessiaCaramello almost 2 years ago - 7 comments

#84 - Add function for spatial community detection

Issue - State: closed - Opened by lassedochreden almost 2 years ago - 3 comments

#83 - Distance to patch

Pull Request - State: closed - Opened by SchulzDan almost 2 years ago - 2 comments

#82 - Fix `ncols` and `nrows` argument in `plotSpatial`

Issue - State: closed - Opened by nilseling almost 2 years ago - 1 comment

#81 - Patch detection update

Pull Request - State: closed - Opened by nilseling almost 2 years ago - 1 comment

#80 - patchDetection fucntion with area output or patch area calculation

Issue - State: closed - Opened by SchulzDan almost 2 years ago - 5 comments

#79 - Customized panel_file is not read correctly with read_steinbock()

Issue - State: closed - Opened by LazDaria almost 2 years ago - 1 comment

#78 - Spatial context functions

Pull Request - State: closed - Opened by lassedochreden almost 2 years ago - 1 comment

#77 - Fixed plotSpatial function

Pull Request - State: closed - Opened by nilseling about 2 years ago

#76 - Adjust edge detection approach

Issue - State: open - Opened by nilseling about 2 years ago

#75 - Bug fix: specify number of nodes in patchDetection

Pull Request - State: closed - Opened by nilseling about 2 years ago - 1 comment

#74 - Fixed int_metadata duplication

Pull Request - State: closed - Opened by nilseling about 2 years ago - 1 comment

#73 - Bug fix: avoid duplication of metadata entries

Pull Request - State: closed - Opened by nilseling about 2 years ago - 1 comment

#72 - duplicated metadata entries

Issue - State: closed - Opened by nilseling about 2 years ago - 3 comments

#71 - KNN - "k must be positive"

Issue - State: closed - Opened by lassedochreden about 2 years ago - 3 comments

#70 - Bug fix: relevel group_by factors

Pull Request - State: closed - Opened by nilseling about 2 years ago

#69 - Re-level factor when calling testInteractions

Issue - State: closed - Opened by nilseling about 2 years ago

#68 - Patch detection fix

Pull Request - State: closed - Opened by nilseling about 2 years ago

#67 - Error when running patchDetection on a SpatialExperiment

Issue - State: closed - Opened by michaeljpitcher about 2 years ago - 9 comments

#66 - Updated for newest imc segmentation pipeline

Pull Request - State: closed - Opened by nilseling over 2 years ago

#65 - Read last entry of metal isotope from file

Pull Request - State: closed - Opened by nilseling over 2 years ago

#64 - Cannot readSCEfromTXT

Issue - State: closed - Opened by l2baeriswyl over 2 years ago - 11 comments

#63 - readSCEfromTXT

Issue - State: closed - Opened by sailseem over 2 years ago - 5 comments

#62 - clustered_neighbors

Issue - State: closed - Opened by sailseem over 2 years ago - 2 comments

#61 - Change regex of readSCEformTXT function

Issue - State: closed - Opened by nilseling over 2 years ago - 4 comments

#60 - Initialize objects with colnames

Issue - State: closed - Opened by nilseling over 2 years ago - 1 comment

#59 - Select files more specifically

Pull Request - State: closed - Opened by nilseling over 2 years ago

#58 - Fixed indexing issue with steinbock graphs

Pull Request - State: closed - Opened by nilseling over 2 years ago

#57 - Error in .steinbock_read_graphs function

Issue - State: closed - Opened by nilseling over 2 years ago - 3 comments

#56 - Read txt fix

Pull Request - State: closed - Opened by nilseling over 2 years ago

#55 - Delaunay

Pull Request - State: closed - Opened by nilseling over 2 years ago

#54 - Compute proximity metrics

Issue - State: open - Opened by nilseling over 2 years ago

#53 - NeighbouRhood files

Issue - State: closed - Opened by aleixriusr over 2 years ago - 3 comments

#52 - Classic bug fix

Pull Request - State: closed - Opened by nilseling over 2 years ago - 1 comment

#51 - Adjust count for classic and patch testInteraction function

Issue - State: closed - Opened by nilseling over 2 years ago - 1 comment

#50 - Figure out if the testInteraction produces symmetric results

Issue - State: closed - Opened by nilseling over 2 years ago - 1 comment

#49 - Restructure

Pull Request - State: closed - Opened by nilseling over 2 years ago - 1 comment

#48 - return output of the permutation tests

Issue - State: closed - Opened by Rcasan over 2 years ago - 2 comments

#47 - Bug fix

Pull Request - State: closed - Opened by nilseling over 2 years ago - 1 comment

#46 - testInteractions() error

Issue - State: closed - Opened by erikgerdtsson over 2 years ago - 7 comments

#45 - Add max distance thresholding to Delaunay triangulation

Issue - State: closed - Opened by nilseling over 2 years ago - 1 comment

#44 - Move all helper functions into a single script

Issue - State: closed - Opened by nilseling over 2 years ago - 1 comment

#43 - Rewrite testInteractions function to increase speed

Issue - State: open - Opened by nilseling over 2 years ago - 1 comment

#42 - Expand unit tests and validity checks

Issue - State: closed - Opened by nilseling over 2 years ago - 4 comments

#41 - Added supervised patch detection function

Pull Request - State: closed - Opened by nilseling over 2 years ago

#40 - Add verbose parameter to testInteractions

Issue - State: closed - Opened by nilseling over 2 years ago - 1 comment

#39 - Check that centroid-0 and centroid-1 fit to X and Y axis

Issue - State: closed - Opened by nilseling over 2 years ago - 2 comments

#38 - Read steinbock metadata from images.csv

Issue - State: closed - Opened by jwindhager almost 3 years ago - 5 comments
Labels: enhancement

#37 - Bioc cleanup

Pull Request - State: closed - Opened by nilseling almost 3 years ago

#36 - Bioc cleanup

Pull Request - State: closed - Opened by nilseling almost 3 years ago

#35 - Bioc cleanup

Pull Request - State: closed - Opened by nilseling almost 3 years ago

#34 - Bioc cleanup

Pull Request - State: closed - Opened by nilseling almost 3 years ago

#33 - First PR for Bioconductor submission

Pull Request - State: closed - Opened by nilseling almost 3 years ago - 1 comment

#32 - Change in steinbock graph file format

Issue - State: closed - Opened by jwindhager almost 3 years ago - 4 comments

#31 - General fixes to address open issues

Pull Request - State: closed - Opened by nilseling almost 3 years ago - 1 comment

#30 - Added neighborhood permutation tests and summary functions

Pull Request - State: closed - Opened by nilseling almost 3 years ago - 1 comment

#29 - Add functions to visualize neighborhoddPermTest results

Issue - State: closed - Opened by nilseling almost 3 years ago - 3 comments

#28 - in `read_cpout` check that channels are not duplicated

Issue - State: closed - Opened by nilseling almost 3 years ago - 1 comment

#27 - Rewrite neighborhood aggregation methods

Issue - State: closed - Opened by nilseling almost 3 years ago - 1 comment

#26 - Implement `findBorderCells` function

Issue - State: closed - Opened by nilseling almost 3 years ago - 1 comment

#25 - Add option to set a maximum distance to knn construction

Issue - State: closed - Opened by nilseling almost 3 years ago - 1 comment

#24 - plotSpatial function

Issue - State: closed - Opened by SchulzDan almost 3 years ago - 5 comments

#23 - Added graph utilities

Pull Request - State: closed - Opened by nilseling almost 3 years ago

#22 - Add option to return proportions when summarizing neighbours

Issue - State: closed - Opened by nilseling almost 3 years ago - 1 comment

#21 - first version of summarizeEnvironment function

Pull Request - State: closed - Opened by SchulzDan almost 3 years ago - 1 comment

#20 - Reader corrections

Pull Request - State: closed - Opened by nilseling about 3 years ago - 2 comments

#19 - Rewrite `readSCEfromTXT` to not require metal names

Issue - State: closed - Opened by nilseling about 3 years ago - 1 comment

#18 - Add simple spatial graph builders

Issue - State: closed - Opened by nilseling about 3 years ago - 3 comments

#17 - Add read_cpout function

Pull Request - State: closed - Opened by nilseling about 3 years ago - 2 comments

#16 - Add things to ImcSegmentationPipeline

Issue - State: closed - Opened by nilseling about 3 years ago - 2 comments

#15 - Read steinbock

Pull Request - State: closed - Opened by nilseling about 3 years ago - 4 comments

#14 - Functions for interfacing with steinbock data

Issue - State: closed - Opened by jwindhager about 3 years ago - 4 comments
Labels: enhancement

#13 - calculateSummary, plotCellCounts fun not found

Issue - State: closed - Opened by mohamadmilad about 3 years ago - 4 comments

#12 - Add function to compensate images

Issue - State: closed - Opened by nilseling about 3 years ago - 1 comment

#11 - Add function to compute minimum distance between each cell and a certain pattern

Issue - State: closed - Opened by nilseling about 3 years ago - 1 comment

#10 - Reforging of the package

Pull Request - State: closed - Opened by PierreBSC over 3 years ago - 1 comment

#9 - Add plotting functions for spatial coordinates and graphs

Issue - State: closed - Opened by nilseling about 4 years ago - 2 comments

#8 - Implement spatial compensation approach from CODEX paper

Issue - State: closed - Opened by nilseling over 4 years ago - 1 comment

#7 - Implement existing spatial analysis methods

Issue - State: closed - Opened by nilseling over 4 years ago - 4 comments

#6 - Reimplement Rphenograph

Issue - State: closed - Opened by nilseling over 4 years ago - 1 comment
Labels: to be discussed

#5 - Create diagnostic functions that visualize the distributions of counts

Issue - State: closed - Opened by nilseling over 4 years ago

#4 - Switch to SingleCellLoomExperiment

Issue - State: closed - Opened by nilseling over 4 years ago - 2 comments

#3 - Write LoomGraph to igraph object

Issue - State: closed - Opened by nilseling over 4 years ago - 1 comment

#2 - Rewrite neighbouRhood

Issue - State: closed - Opened by nilseling over 4 years ago - 1 comment

GitHub / BodenmillerGroup/imcRtools issues and pull requests