glmGamPoi

glmGamPoi copied to clipboard

Can't install the package on MacOS Monterey

1

Hi, I noticed in the error message below it mentioned "big sur" which was the previous MacOS version. Is that why my installation kept failing? Thanks! JS BiocManager::install("glmGamPoi") 'getOption("repos")' replaces...

sjwu571

Core Usage

1

Hello! Insanely useful package. Thank you so much for this! I wanted to ask, when fitting a model with glm_gp on slightly larger datasets, during the final fitting step, all...

NKalavros

Too many DEGs?

1

Hi, I am a fresh user of glmGamPoi and thanks for providing this awesome tool! I tried to identify DEGs in scRNA and successfully run the following code: ``` load('/Volumes/kfsd/GSE200903_new_combined_cluster_FibroSamples_2022-01-14.RData')...

KunFang93

test_de failing with on_disk models

4

Hello Constantin, Thank you for this code, I've been using and learning more about it for several months. I'm working with some large data sets and using glmGamPoi to perform...

NathanSiemers

determining the less trustworthy log2fc values

4

Hello, thanks very much for your package. I just want to follow up on this point from the vignette: > The large `lfc` values come from groups were nearly all...

ceesu

pseudobulk_by apparently dropping columns

1

Hi, I am successfully using your package with scRNA-Seq data, but finding a possible bug when trying out the `pseudobulk_by` option. Below I show it working fine without `pseudobulk_by` and...

malcook

Use for pseudobulk differential expression - advantages & logFC values

1

Hi, Thank you for your very useful package. I have two questions regarding its use for pseudobulk differential expression analysis. Firstly, could you outline the reasons why you think your...

Al-Murphy

Return standard error of coefficient estimates

9

In https://github.com/mikelove/DESeq2/issues/29 @mschubert raised the point that `glmGamPoi`, unlike `DESeq2` does not return the standard error for the LFC estimates. His use-case for them is change point detection, where he...

const-ae

Tests fail on i386 (really i686): ailure: qres.gampoi can handle other weird values (@test-residuals.R#112) `a` is not strictly more than `b`. Difference: 0

3

Hello, While packaging glmgampoi for Debian we noticed that the tests fail on 32bit x86 ``` BEGIN TEST testthat.R R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020...

mr-c

installation of package ‘glmGamPoi’ had non-zero exit status

6

Hello, I am unable to install glmGamPoi on my intel mac locally on R. `if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("glmGamPoi")` I get the error message after installing from source:...

NicoHadas