MarioniLab miloR issues

MarioniLab / miloR

R package implementation of Milo for testing for differential abundance in KNN graphs

https://bioconductor.org/packages/release/bioc/html/miloR.html

GNU General Public License v3.0

315 stars 20 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

No Significant Neighbourhoods Result is Error

#342 DarioS closed 5 days ago
1
makeNhoods graph refinement (issue with isolated vertices)

#341 mdpatric closed 6 days ago
4
Import precomputed graph

#340 Dannyxu123 opened 1 week ago
7
Existence of 2 tuitorials for the "Differential abundance testing with Milo - Mouse gastrulation example"

#339 JesseRop opened 1 week ago
3
Direction of test for logFC calculation

#338 RemiDL opened 1 week ago
1
How to use MiloR after subsetting the cell types from total cell types?

#337 mainharryHR opened 1 week ago
4
Log10 FC or Log2 FC?

#336 mainharryHR opened 1 week ago
1
Does MiloR take into account that the two compared conditions have different number of cells?

#335 crodriguezres opened 2 weeks ago
2
Fix for #328

#334 MikeDMorgan closed 4 weeks ago
0
Multiple comparisons gives identical results by using model.contrasts

#333 mainharryHR closed 4 weeks ago
12
object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance

#332 shuaizh117 closed 4 weeks ago
2
Progress Bar for GLMM

#331 DarioS closed 1 week ago
6
nhood size distribution: some neighbourhoods have over 2000 cells

#330 YiweiNiu closed 1 month ago
4
merge devel - alignment with Bioc 3.19 version + bug fix

#329 MikeDMorgan closed 1 month ago
0
Function Not Found Error

#328 DarioS closed 4 weeks ago
3
Cell type is lost during annotateNhoods

#327 carlacohen closed 3 weeks ago
5
Prevention of Neighbourhood Merging of Similar Cell Types into Neighbourhood Groups

#326 DarioS closed 1 month ago
1
Cell Condition Relabelling Functionality

#325 DarioS closed 3 weeks ago
3
Lack of Robustness to Missing Values in Dependent Variable

#324 DarioS closed 1 month ago
3
GLMM vignette

#323 CarrieMeeks closed 1 month ago
3
Applicability to Cancer Samples

#322 DarioS closed 1 month ago
1
Error in `scale_color_gradient2()`

#321 ShashTrip1 opened 1 month ago
5
Can't interpret plotNhoodGraphDA and plotUMAP

#320 giuditta2024 closed 2 months ago
2
Inconsistent Default Values Between Functions

#319 DarioS closed 2 months ago
2
Predefined Graph Import Still Not Available to Use

#318 DarioS opened 2 months ago
4
Design matrix and nhood counts are not the same dimension

#317 nbutyrate opened 2 months ago
1
da_results error

#316 pitos21 closed 2 months ago
6
Seeking Guidance on Input Data for PCA Reduction and Gene Expression in Milo

#315 tim-meese closed 2 months ago
2
Error: (converted from warning) 'as(<dgTMatrix>, "dgCMatrix")' is deprecated.

#314 Lil-5 opened 3 months ago
4
Results Changed

#313 ShashTrip1 opened 3 months ago
2
makeNhoods missing cell ids

#312 flde closed 3 months ago
2
Reorder Ident in plotDAbeeswarm

#311 ShashTrip1 opened 3 months ago
4
Milo not identifying significant results

#310 RunyuXia closed 2 months ago
8
plotNhoodGraphDA does not display logFC data

#309 tnystul opened 4 months ago
2
Color scale missing (res_column) in plotNhoodGraphDA()

#308 KatjaRM closed 4 months ago
2
error in makeNhoods

#307 GrigoriiNos opened 4 months ago
3
How to extract cell barcode identified by MiloR?

#306 obotman closed 4 months ago
2
How to implement more complex contrast formulas

#305 CarlottaHS opened 5 months ago
5
Update contrasts documentation

#304 MikeDMorgan closed 4 weeks ago
0
First level loss when running testNhoods with multiple contrasts and multiple batch

#303 Tang-RH closed 5 months ago
3
Use milo with continuous variable

#302 RunyuXia closed 4 months ago
1
plotNhoodSizeHist not lining up with nhoodCounts

#301 LinearParadox closed 5 months ago
2
scVI corrected dimensions with MiloR

#300 LinearParadox opened 5 months ago
1
Choice of fdr.weighting in testNhoods

#299 bazelep opened 6 months ago
2
fix REML score vector bug and remove sparse -> dense coercion slow down

#298 MikeDMorgan closed 6 months ago
0
Mixed effects models with contrasts

#297 HJ234 closed 7 months ago
2
findNhoodGroupMarkers: overlapping nhoods in fake.meta

#296 gianfilippo closed 7 months ago
2
Add NB-GLMM to master branch.

#295 MikeDMorgan closed 7 months ago
1
when should buildGraph be used with transposed=TRUE?

#294 noranekonobokkusu closed 7 months ago
4
Can I run calcNhoodDistance before countCells

#293 yulijia opened 8 months ago
3