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

GitHub / marionilab/miloR issues and pull requests