neurorestore Libra issues

neurorestore / Libra

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Wrong avg_logFC?

#69 JerryZhang-1222 opened 1 week ago
0
Error in base::rowMeans(x, na.rm = na.rm, dims = dims, ...) : 'x' must be an array of at least two dimensions

#68 AnaisJulien opened 2 weeks ago
0
ArchR project input

#67 mjleone opened 1 month ago
0
Recommendations for filtering scATAC-seq pseudobulk data

#66 blake-bowen opened 1 month ago
0
Could you add latent variable support for DESEQ2 and edgeR?

#65 ilya-strunilin opened 1 month ago
0
Column `cell_type` is not found. Run `rlang::last_trace()` to see where the error occurred.

#64 tsjzz opened 1 month ago
0
Question for the results of singlecell::MAST

#63 yecotoo opened 1 month ago
0
Column pct.1 doesn't exist

#62 yecotoo closed 2 months ago
2
Error in `group_by()`: ! Must group by variables found in `.data`. ✖ Column `cell_type` is not found.

#61 yecotoo closed 2 months ago
16
Error in group_by(): ! Must group by variables found in .data. ✖ Column cell_type is not found.

#60 yecotoo closed 2 months ago
1
Error in h(simpleError(msg, call)): Error in calculating parameter "x" when selecting method for function "rowSums": subscript out of bounds In addition: Warning message: Layer ‘data' is empty.

#59 yecotoo closed 3 months ago
9
Fix Issue #49

#58 Random-x-1 opened 3 months ago
0
Unclear Approach to Groups Comparison

#57 DarioS opened 4 months ago
0
Question about batch effect correction

#56 1226235 opened 5 months ago
2
Error in `$<-.data.frame`(`*tmp*`, "replicate", value = integer(0))

#55 yuanG2000 opened 6 months ago
14
Is it possible to add pct.1 / pct.2 column in the result?

#54 jamesbangbang1126 opened 6 months ago
1
Mixed model methods retuning only one cell type.

#53 brianherb opened 6 months ago
1
How to correct for age, sex, etc.?

#52 yesitsjess opened 7 months ago
1
Error: Column `cell_type` is not found

#51 jamesonholloman opened 8 months ago
6
The dataset used for the demonstration `hagai_toy` reported an error

#50 Taoo777 opened 8 months ago
3
Error in (function (cl, name, valueClass) : "data" is not a slot in the "Assay5" category.

#49 Pigeongeon opened 9 months ago
3
Reference level of `label_col` factor not respected

#48 agrier-wcm opened 10 months ago
1
How to determine two comparison groups

#47 yanwuanxin opened 11 months ago
0
“Column `cell_type` is not found.”

#46 ltj-github opened 11 months ago
5
All p.val are N.A. for mixedmodel

#45 DelongZHOU closed 11 months ago
2
Something about the delay

#44 JianSongHuang opened 1 year ago
0
Error when no cells present in one condition cell type

#43 mhvbyrne opened 1 year ago
1
Issue of avg_logFC in pseudobulk RNA seq output file

#42 jujurring opened 1 year ago
3
A quick question about application of liner mixed model method to detect degs

#41 HelloWorldLTY opened 1 year ago
7
NA values when using mixedmodel for deg identificaiton.

#40 HelloWorldLTY opened 1 year ago
0
Some questions about mixed model

#39 HelloWorldLTY opened 1 year ago
2
How to generate the pseudobulk datasets in this paper?

#38 HelloWorldLTY opened 1 year ago
4
input of run_de function when using a Seurat object

#37 pandaqiuqiu opened 1 year ago
10
run_de function is not found.

#36 elifozcelik opened 1 year ago
4
2 bulk_rnaseq datasets on Zenodo are missing

#35 Nayrouz109 opened 1 year ago
1
Can we speed up run_de with mixed models ?

#34 Nayrouz109 closed 1 year ago
2
How to get a relative high confidence results in the circumstance of using a imbalanced data

#33 thecatgonewithwid opened 2 years ago
1
Design order and account batch effect

#32 VergaJU closed 3 months ago
8
Some Thing Wrong with DESeq2 and Limma?

#31 hjh-air-cond closed 2 years ago
4
How to perform edgeR-LRT using Libra with no biological replicates?

#30 DrDaedalusWHU opened 2 years ago
2
min_feature option in run_de not working

#29 Peter-bbh closed 2 years ago
7
Feature request: percentage expressed

#28 GBeattie opened 2 years ago
1
Replication, Label, and Cell Type for DEG

#27 Sayyam-Shah opened 2 years ago
4
Just wanna be sure about the result.

#26 hjh-air-cond opened 2 years ago
2
Accounting for covariates

#25 smorabit closed 2 years ago
2
Could not find function "run_de"

#24 venchi9 opened 2 years ago
6
Libra - singlecell giving opposite results

#23 saisomesh2594 opened 2 years ago
1
What is 'label' and 'replication' in my single-cell datasets?

#22 victorwang123 opened 2 years ago
1
edgeR analysis not preserving the level and order information of the Cell_type

#21 RobertWhitener opened 2 years ago
5
Keeping the Gene names when calculating delta Variance

#20 RobertWhitener opened 2 years ago
2