MarioniLab/miloR

Issues

• plotNhoodGraphDA does not display logFC data

  #309 opened 2 months ago by tnystul
  2

• Does MiloR take into account that the two compared conditions have different number of cells?

  #335 opened 2 months ago by crodriguezres
  2

• Gene expression testing of only DA neighborhoods within group??

  #345 opened 2 months ago by carl-coyle
  4

• Error: (converted from warning) 'as(<dgTMatrix>, "dgCMatrix")' is deprecated.

  #314 opened 8 months ago by Lil-5
  8

• Error in S4Vectors

  #348 opened 3 months ago by avfentor
  0

• buildGraph error

  #347 opened 3 months ago by yangjie4546
  3

• Error in `scale_color_gradient2()`

  #321 opened 6 months ago by ShashTrip1
  10

• Can you implement a complete miloR in python ?

  #346 opened 4 months ago by yitengfei120011
  1

• How to use MiloR after subsetting the cell types from total cell types?

  #337 opened 4 months ago by mainharryHR
  4

• MiloR in spatial transcriptomics data

  #344 opened 4 months ago by zeniazen5
  1

• Mass cytometry data

  #343 opened 4 months ago by NicoFuenza
  1

• No Significant Neighbourhoods Result is Error

  #342 opened 5 months ago by DarioS
  1

• makeNhoods graph refinement (issue with isolated vertices)

  #341 opened 5 months ago by mdpatric
  4

• Import precomputed graph

  #340 opened 5 months ago by Dannyxu123
  7

• Existence of 2 tuitorials for the "Differential abundance testing with Milo - Mouse gastrulation example"

  #339 opened 5 months ago by JesseRop
  3

• Progress Bar for GLMM

  #331 opened 5 months ago by DarioS
  6

• Direction of test for logFC calculation

  #338 opened 5 months ago by RemiDL
  1

• Log10 FC or Log2 FC?

  #336 opened 5 months ago by mainharryHR
  1

• Multiple comparisons gives identical results by using model.contrasts

  #333 opened 6 months ago by mainharryHR
  12

• Cell type is lost during annotateNhoods

  #327 opened 6 months ago by carlacohen
  5

• Cell Condition Relabelling Functionality

  #325 opened 6 months ago by DarioS
  3

• Update contrasts documentation

  #304 opened 6 months ago by MikeDMorgan
  0

• Function Not Found Error

  #328 opened 6 months ago by DarioS
  3

• object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance

  #332 opened 6 months ago by shuaizh117
  2

• How to implement more complex contrast formulas

  #305 opened 10 months ago by CarlottaHS
  5

• Prevention of Neighbourhood Merging of Similar Cell Types into Neighbourhood Groups

  #326 opened 6 months ago by DarioS
  1

• nhood size distribution: some neighbourhoods have over 2000 cells

  #330 opened 6 months ago by YiweiNiu
  4

• Lack of Robustness to Missing Values in Dependent Variable

  #324 opened 6 months ago by DarioS
  3

• Inconsistent Default Values Between Functions

  #319 opened 7 months ago by DarioS
  2

• GLMM vignette

  #323 opened 6 months ago by CarrieMeeks
  3

• Applicability to Cancer Samples

  #322 opened 6 months ago by DarioS
  1

• Can't interpret plotNhoodGraphDA and plotUMAP

  #320 opened 7 months ago by GiudittaClerici
  2

• Milo not identifying significant results

  #310 opened 7 months ago by RunyuXia
  8

• Predefined Graph Import Still Not Available to Use

  #318 opened 7 months ago by DarioS
  4

• da_results error

  #316 opened 7 months ago by pitos21
  6

• Design matrix and nhood counts are not the same dimension

  #317 opened 7 months ago by nbutyrate
  1

• Seeking Guidance on Input Data for PCA Reduction and Gene Expression in Milo

  #315 opened 7 months ago by tim-meese
  2

• Reorder Ident in plotDAbeeswarm

  #311 opened 8 months ago by ShashTrip1
  4

• Results Changed

  #313 opened 8 months ago by ShashTrip1
  2

• makeNhoods missing cell ids

  #312 opened 8 months ago by flde
  2

• Color scale missing (res_column) in plotNhoodGraphDA()

  #308 opened 9 months ago by KatjaRM
  2

• Use milo with continuous variable

  #302 opened 9 months ago by RunyuXia
  1

• error in makeNhoods

  #307 opened 9 months ago by GrigoriiNos
  3

• How to extract cell barcode identified by MiloR?

  #306 opened 9 months ago by obotman
  2

• First level loss when running testNhoods with multiple contrasts and multiple batch

  #303 opened 10 months ago by Tang-RH
  3

• plotNhoodSizeHist not lining up with nhoodCounts

  #301 opened 10 months ago by LinearParadox
  2

• Choice of fdr.weighting in testNhoods

  #299 opened a year ago by bazelep
  2

• scVI corrected dimensions with MiloR

  #300 opened 10 months ago by LinearParadox
  1

• Mixed effects models with contrasts

  #297 opened a year ago by HJ234
  2

• findNhoodGroupMarkers: overlapping nhoods in fake.meta

  #296 opened a year ago by gianfilippo
  2