Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / marionilab/miloR issues and pull requests
#348 - Error in S4Vectors
Issue -
State: open - Opened by avfentor 27 days ago
#347 - buildGraph error
Issue -
State: open - Opened by yangjie4546 about 1 month ago
- 3 comments
#346 - Can you implement a complete miloR in python ?
Issue -
State: closed - Opened by yitengfei120011 2 months ago
- 1 comment
#345 - Gene expression testing of only DA neighborhoods within group??
Issue -
State: open - Opened by carl-coyle 2 months ago
- 3 comments
#344 - MiloR in spatial transcriptomics data
Issue -
State: open - Opened by zeniazen5 3 months ago
- 1 comment
#343 - Mass cytometry data
Issue -
State: open - Opened by NicoFuenza 3 months ago
- 1 comment
#342 - No Significant Neighbourhoods Result is Error
Issue -
State: closed - Opened by DarioS 3 months ago
- 1 comment
#341 - makeNhoods graph refinement (issue with isolated vertices)
Issue -
State: closed - Opened by mdpatric 3 months ago
- 4 comments
#340 - Import precomputed graph
Issue -
State: open - Opened by Dannyxu123 3 months ago
- 7 comments
#339 - Existence of 2 tuitorials for the "Differential abundance testing with Milo - Mouse gastrulation example"
Issue -
State: open - Opened by JesseRop 3 months ago
- 3 comments
#338 - Direction of test for logFC calculation
Issue -
State: open - Opened by RemiDL 3 months ago
- 1 comment
#337 - How to use MiloR after subsetting the cell types from total cell types?
Issue -
State: closed - Opened by mainharryHR 3 months ago
- 4 comments
#336 - Log10 FC or Log2 FC?
Issue -
State: open - Opened by mainharryHR 3 months ago
- 1 comment
#335 - Does MiloR take into account that the two compared conditions have different number of cells?
Issue -
State: open - Opened by crodriguezres 4 months ago
- 2 comments
#334 - Fix for #328
Pull Request -
State: closed - Opened by MikeDMorgan 4 months ago
#333 - Multiple comparisons gives identical results by using model.contrasts
Issue -
State: closed - Opened by mainharryHR 4 months ago
- 12 comments
#332 - object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance
Issue -
State: closed - Opened by shuaizh117 4 months ago
- 2 comments
#331 - Progress Bar for GLMM
Issue -
State: closed - Opened by DarioS 4 months ago
- 6 comments
#330 - nhood size distribution: some neighbourhoods have over 2000 cells
Issue -
State: closed - Opened by YiweiNiu 4 months ago
- 4 comments
#329 - merge devel - alignment with Bioc 3.19 version + bug fix
Pull Request -
State: closed - Opened by MikeDMorgan 4 months ago
#328 - Function Not Found Error
Issue -
State: closed - Opened by DarioS 4 months ago
- 3 comments
Labels: bug
#327 - Cell type is lost during annotateNhoods
Issue -
State: closed - Opened by carlacohen 5 months ago
- 5 comments
#326 - Prevention of Neighbourhood Merging of Similar Cell Types into Neighbourhood Groups
Issue -
State: closed - Opened by DarioS 5 months ago
- 1 comment
#325 - Cell Condition Relabelling Functionality
Issue -
State: closed - Opened by DarioS 5 months ago
- 3 comments
#324 - Lack of Robustness to Missing Values in Dependent Variable
Issue -
State: closed - Opened by DarioS 5 months ago
- 3 comments
#323 - GLMM vignette
Issue -
State: closed - Opened by CarrieMeeks 5 months ago
- 3 comments
#322 - Applicability to Cancer Samples
Issue -
State: closed - Opened by DarioS 5 months ago
- 1 comment
#321 - Error in `scale_color_gradient2()`
Issue -
State: open - Opened by ShashTrip1 5 months ago
- 10 comments
#320 - Can't interpret plotNhoodGraphDA and plotUMAP
Issue -
State: closed - Opened by GiudittaClerici 5 months ago
- 2 comments
#319 - Inconsistent Default Values Between Functions
Issue -
State: closed - Opened by DarioS 6 months ago
- 2 comments
#318 - Predefined Graph Import Still Not Available to Use
Issue -
State: open - Opened by DarioS 6 months ago
- 4 comments
Labels: documentation
#317 - Design matrix and nhood counts are not the same dimension
Issue -
State: open - Opened by nbutyrate 6 months ago
- 1 comment
#316 - da_results error
Issue -
State: closed - Opened by pitos21 6 months ago
- 6 comments
#315 - Seeking Guidance on Input Data for PCA Reduction and Gene Expression in Milo
Issue -
State: closed - Opened by tim-meese 6 months ago
- 2 comments
#314 - Error: (converted from warning) 'as(<dgTMatrix>, "dgCMatrix")' is deprecated.
Issue -
State: open - Opened by Lil-5 7 months ago
- 8 comments
#313 - Results Changed
Issue -
State: open - Opened by ShashTrip1 7 months ago
- 2 comments
#312 - makeNhoods missing cell ids
Issue -
State: closed - Opened by flde 7 months ago
- 2 comments
#311 - Reorder Ident in plotDAbeeswarm
Issue -
State: open - Opened by ShashTrip1 7 months ago
- 4 comments
#310 - Milo not identifying significant results
Issue -
State: closed - Opened by RunyuXia 7 months ago
- 8 comments
#309 - plotNhoodGraphDA does not display logFC data
Issue -
State: open - Opened by tnystul 7 months ago
- 2 comments
#308 - Color scale missing (res_column) in plotNhoodGraphDA()
Issue -
State: closed - Opened by KatjaRM 7 months ago
- 2 comments
#307 - error in makeNhoods
Issue -
State: open - Opened by GrigoriiNos 8 months ago
- 3 comments
#306 - How to extract cell barcode identified by MiloR?
Issue -
State: closed - Opened by obotman 8 months ago
- 2 comments
#305 - How to implement more complex contrast formulas
Issue -
State: open - Opened by CarlottaHS 8 months ago
- 5 comments
#304 - Update contrasts documentation
Issue -
State: closed - Opened by MikeDMorgan 9 months ago
Labels: documentation
#303 - First level loss when running testNhoods with multiple contrasts and multiple batch
Issue -
State: closed - Opened by Tang-RH 9 months ago
- 3 comments
#302 - Use milo with continuous variable
Issue -
State: closed - Opened by RunyuXia 9 months ago
- 1 comment
#301 - plotNhoodSizeHist not lining up with nhoodCounts
Issue -
State: closed - Opened by LinearParadox 9 months ago
- 2 comments
#300 - scVI corrected dimensions with MiloR
Issue -
State: open - Opened by LinearParadox 9 months ago
- 1 comment
#299 - Choice of fdr.weighting in testNhoods
Issue -
State: open - Opened by bazelep 9 months ago
- 2 comments
#298 - fix REML score vector bug and remove sparse -> dense coercion slow down
Pull Request -
State: closed - Opened by MikeDMorgan 10 months ago
#297 - Mixed effects models with contrasts
Issue -
State: closed - Opened by HJ234 10 months ago
- 2 comments
#296 - findNhoodGroupMarkers: overlapping nhoods in fake.meta
Issue -
State: closed - Opened by gianfilippo 11 months ago
- 2 comments
#295 - Add NB-GLMM to master branch.
Pull Request -
State: closed - Opened by MikeDMorgan 11 months ago
- 1 comment
#294 - when should buildGraph be used with transposed=TRUE?
Issue -
State: closed - Opened by noranekonobokkusu 11 months ago
- 4 comments
#293 - Can I run calcNhoodDistance before countCells
Issue -
State: open - Opened by yulijia 11 months ago
- 3 comments
#292 - Please close this question
Issue -
State: closed - Opened by MoLuLuMo 11 months ago
#291 - testNhoods() returns :Error in glmFit.default(y, design = design, dispersion = dispersion, offset = offset, : NA dispersions not allowed
Issue -
State: closed - Opened by zzzzjb about 1 year ago
- 5 comments
#290 - Problem in buildNhoodGraph on a large dataset
Issue -
State: open - Opened by moinfar about 1 year ago
- 5 comments
#289 - Introduce Milo NB-GLMM to devel
Pull Request -
State: closed - Opened by MikeDMorgan about 1 year ago
- 1 comment
#288 - SpatialFDR after testNhoods() is NA
Issue -
State: closed - Opened by aodainic7 about 1 year ago
- 4 comments
#287 - Simple question "Can we add seurat_clusters"?
Issue -
State: closed - Opened by mckimcd177 about 1 year ago
- 1 comment
#286 - Include batch as a covariate or use batch-corrected latent space for constructing KNN graph
Issue -
State: closed - Opened by lucygarner about 1 year ago
- 3 comments
#285 - When dealing with multiple samples in RDS, should we opt for reduced dimensionality using 'HARMONY' or stick with PCA?
Issue -
State: closed - Opened by hai178912522 over 1 year ago
- 3 comments
#284 - could this packages support TSNE?
Issue -
State: closed - Opened by ZivTQ over 1 year ago
- 2 comments
#283 - findNhoodMarkers mixing Gene names
Issue -
State: closed - Opened by Dario-Rocha over 1 year ago
- 1 comment
#282 - Plotting LFC without filtering by FDR
Issue -
State: closed - Opened by Dario-Rocha over 1 year ago
- 1 comment
#281 - MiloR on compositional data
Issue -
State: closed - Opened by Dario-Rocha over 1 year ago
- 1 comment
#280 - Nhood graph plotting respect factor variables
Pull Request -
State: closed - Opened by MikeDMorgan over 1 year ago
- 1 comment
#279 - plotNhoodGraph doesn't respect factor variables
Issue -
State: closed - Opened by MikeDMorgan over 1 year ago
#278 - runPCA error
Issue -
State: closed - Opened by pc2001 over 1 year ago
- 9 comments
#277 - Error In buildGraph
Issue -
State: closed - Opened by connerlambden over 1 year ago
- 2 comments
#276 - DA test found NO SpatialFDR (<0.05) in two groups
Issue -
State: closed - Opened by Rainjie-afk over 1 year ago
- 1 comment
#275 - Should I consider RNA assay or Integrated Assay for Milo
Issue -
State: closed - Opened by deconvolute over 1 year ago
- 5 comments
#274 - Annotation on plotNhoodExpressionGroups()?
Issue -
State: closed - Opened by mdeea over 1 year ago
- 1 comment
#272 - Error message with findNhoodGroupMarkers
Issue -
State: closed - Opened by gianfilippo over 1 year ago
- 8 comments
#271 - testNhoods with multiple contrasts
Issue -
State: closed - Opened by gianfilippo over 1 year ago
- 5 comments
#270 - merging Nhood with logFC of opposite sign
Issue -
State: open - Opened by gianfilippo over 1 year ago
- 15 comments
Labels: bug
#268 - support for time points from same donor
Issue -
State: open - Opened by zia1138 over 1 year ago
- 11 comments
#267 - Call to deprecated Matrix function in calcNhoodDistance()
Issue -
State: closed - Opened by mdeea over 1 year ago
- 8 comments
#266 - Error when using Build Graph
Issue -
State: closed - Opened by eseffar over 1 year ago
- 1 comment
#265 - effect of k and N of PCs on DA analysis
Issue -
State: closed - Opened by gianfilippo over 1 year ago
- 3 comments
#264 - Error in comparison of two samples
Issue -
State: closed - Opened by Yingjie848 over 1 year ago
- 6 comments
#263 - Design matrix not full rank - mixture of paired and unpaired samples
Issue -
State: closed - Opened by kane9530 over 1 year ago
- 1 comment
#262 - no SpatialFDR generated
Issue -
State: closed - Opened by parkjooyoung99 over 1 year ago
- 1 comment
#261 - Nhoodgroups change when code is re-run
Issue -
State: closed - Opened by caitsimop over 1 year ago
- 2 comments
#260 - List of cells that are part of a neighbourhood of interest highlighted by testNhoods()
Issue -
State: closed - Opened by GAgafencu over 1 year ago
- 2 comments
#259 - Recommendation for using Milo for pooled CRISPR screens
Issue -
State: closed - Opened by joschif over 1 year ago
- 3 comments
#256 - fixing missing NA issue in beeswarm plot
Pull Request -
State: closed - Opened by emdann over 1 year ago
- 1 comment
#254 - Continuous variables and ANOVAs?
Issue -
State: closed - Opened by dagarfield almost 2 years ago
- 1 comment
#247 - Sensitivity on rare cell population
Issue -
State: closed - Opened by BingjieZhang almost 2 years ago
- 3 comments
#246 - Added function to visualize the number of neighboring cells per condition and neighborhood
Pull Request -
State: closed - Opened by nickhir almost 2 years ago
- 5 comments
#238 - What if I don't see a significant difference in abundance?
Issue -
State: closed - Opened by jbrandst7 about 2 years ago
- 2 comments
#234 - Error running testNhoods from Tutorial
Issue -
State: closed - Opened by gt7901b about 2 years ago
- 6 comments
#222 - testNhoods generate the error message: Error in if (median(f75) < 1e-20) { : missing value where TRUE/FALSE needed
Issue -
State: closed - Opened by ScarlettQGG over 2 years ago
- 8 comments
#221 - Genetic case
Pull Request -
State: closed - Opened by MikeDMorgan over 2 years ago
- 1 comment
#219 - Adding informative error message for plotDAbeeswarm when no significant results at SpatialFDR < 0.1
Issue -
State: closed - Opened by emdann over 2 years ago
- 2 comments
#207 - Patch for no overlap edge case with graph-based spatialFDR
Pull Request -
State: closed - Opened by emdann over 2 years ago
- 2 comments
#204 - Issue with R implementation
Issue -
State: closed - Opened by jrgehlha over 2 years ago
- 2 comments
#196 - SpatialFDR has same value in da_results
Issue -
State: closed - Opened by LeoCao-X over 2 years ago
- 1 comment