bodenmillergroup/imcdataanalysis issues and pull requests

#104 - Writing out compensated images as TIFF files

Issue - State: closed - Opened by rahilgholami 4 months ago - 3 comments

#103 - Running stats on marker expression between groups

Issue - State: closed - Opened by rebekahdadey 6 months ago - 1 comment

#102 - Phenograph Clustering

Issue - State: closed - Opened by tbudiman7 9 months ago - 1 comment

#100 - Marker disappeared in the heatmap

Issue - State: closed - Opened by giuliospinozzi 11 months ago - 4 comments

#99 - Data availability

Issue - State: closed - Opened by jcasadogp 11 months ago - 1 comment

#98 - Using IMCDataAnalysis with HistoCAT-exported Data

Issue - State: closed - Opened by sbeber16 12 months ago - 1 comment

#97 - train-classifier

Issue - State: closed - Opened by SimonSichone 12 months ago - 3 comments

#96 - Updated plotCells object scaling

Pull Request - State: open - Opened by lassedochreden 12 months ago

#95 - no detected spatial_community, empty heatmap

Issue - State: closed - Opened by Elena983 about 1 year ago - 7 comments

#94 - Problem with confusion matrix

Issue - State: closed - Opened by RiccardoSin about 1 year ago - 3 comments

#93 - Problem with concatenation

Issue - State: closed - Opened by GiCarlu about 1 year ago - 2 comments

#92 - Analysis workflow for IMC data after segmentation in HALO

Issue - State: closed - Opened by alexeykb about 1 year ago - 2 comments

#91 - Read in and consolidate labeled data(remove-doublets)phenotyping section.

Issue - State: closed - Opened by SimonSichone about 1 year ago - 4 comments

#90 - Subset the SPE object for cell-level visualization

Issue - State: open - Opened by nilseling about 1 year ago
Labels: enhancement

#89 - 8.3 Seurat correction - problems

Issue - State: closed - Opened by GiCarlu about 1 year ago - 3 comments

#88 - packages dosen't contain needed functions

Issue - State: closed - Opened by GiCarlu about 1 year ago - 2 comments

#87 - cytoviewer citation update

Pull Request - State: closed - Opened by lassedochreden about 1 year ago - 2 comments

#86 - Update DEVELOPMENT.md

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

#85 - Devel

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

#84 - Also visualize the CN heatmap without column scaling

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

#83 - Question about batch effect correction

Issue - State: closed - Opened by EmilyZou123 about 1 year ago - 7 comments

#82 - Normalize is defunct

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

#81 - Number of cell for each sample

Issue - State: closed - Opened by giuliospinozzi over 1 year ago - 1 comment

#80 - Same sample colors between different heatmaps

Issue - State: closed - Opened by giuliospinozzi over 1 year ago - 1 comment

#79 - Subclustering of PhenoGraph clusters

Issue - State: closed - Opened by marleneweiss over 1 year ago - 12 comments

#78 - 12.1 Spatial Interaction Graphs: No graph, only title

Issue - State: closed - Opened by Will760 over 1 year ago - 2 comments

#77 - 11.2.1 Visualizing metadata: Error in .valid.colour(...)

Issue - State: closed - Opened by Will760 over 1 year ago - 2 comments

#76 - 10.4.1 Publication-ready ComplexHeatmap not generating anything but no errors

Issue - State: closed - Opened by Will760 over 1 year ago - 4 comments

#75 - silhouette width score (Cell Phenotyping)

Issue - State: closed - Opened by wqcho00 over 1 year ago - 2 comments

#74 - Fast MNN batch correction: more singular values/vectors requested than available

Issue - State: closed - Opened by Will760 over 1 year ago - 2 comments

#73 - Process a single ROI

Issue - State: closed - Opened by giuliospinozzi over 1 year ago - 1 comment

#72 - PlotPixels: Segmentation masks must only contain integer values

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

#71 - How to exclude an image from analysis if cell density is too low.

Issue - State: closed - Opened by Will760 over 1 year ago - 3 comments

#70 - Tests to setup Docker on macOS runner

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

#69 - Devel

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

#68 - Set the seed for clustering

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

#67 - Add more information how to set the seed in detectCommunities

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

#66 - Unusually low marker expression?

Issue - State: closed - Opened by Yanira1208 over 1 year ago - 2 comments

#65 - spillover correction

Issue - State: closed - Opened by rahilgholami over 1 year ago - 10 comments

#64 - Updates for resubmission

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

#63 - Add cytoviewer to workflow

Issue - State: closed - Opened by lassedochreden over 1 year ago - 1 comment

#62 - Construction of spatial graphs for neighbourhood analysis

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

#61 - Error when performing fastMNN batch correction

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

#60 - Any idea why the last error occurs?

Issue - State: closed - Opened by StiThor over 1 year ago - 7 comments

#59 - Imaging mass cytometry data analysis

Issue - State: closed - Opened by StiThor over 1 year ago - 14 comments

#58 - Fixes to pass checks

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

#57 - One of my gated cells is missing (9.3 Classification Approach)

Issue - State: closed - Opened by zoqaiyum over 1 year ago - 1 comment

#56 - Run normalize with only 1 sample

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

#55 - Transformation of IMC data

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