batchelor
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LTLA
Clone of the Bioconductor repository for the batchelor package.
Hello, thank you for the amazing package! However we ran into some issue when I was running `reducedMNN()` with my own PCA embeddings. I hit an error saying ERROR: C...
(First, thanks Aaron for the development and maintenance of this awesome package!) After reading this [preprint](https://www.biorxiv.org/content/early/2023/07/07/2023.07.07.548105.abstract), I was wondering if there would be the possibility for such a semi-supervised correction...
Hi, great package. I was wondering if this form of batch integration is also applicable to bulk RNA-Seq data. Sure the data is less sparse, but would that be an...
Hello, I have an issue with the 'fastMNN' function in batchelor. I can't access the assay of the generated object as I get an error. ```r out= batchelor::fastMNN(objects.sce) out ```...
Similar to https://github.com/LTLA/BiocNeighbors/issues/21, https://github.com/LTLA/csaw/issues/21, and https://github.com/LTLA/metapod/issues/1. See details of the failure on the Mac arm64 semiweekly report: https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/batchelor/kjohnson1-checksrc.html As a consequence, there's no Mac arm64 binary in BioC 3.18: https://bioconductor.org/packages/3.18/batchelor...
Hi, when I use `multiBatchNorm` to do normalization and adjust for the sequencing depth, I tried to figure out it by changing the argument `min.mean`, but it cannot work. And...
Hello, Thank you for this great tool. I'm working to analyze multiple samples from different conditions and compare to published data, in total there are 240k cells over ~40 samples....
Dear Developer, I wanna ask about an error occurred when I run the fastMNN > out
Hi MNN group, I see in the MNN help pages that it is not recommended to use MNN-corrected gene expression matrix for quantitative analysis such as differential gene expression. But...
Hello, I am running fastMNN with data set that having 2 batches , 'dataset' and 'condition' . I tried to correct both in once by specifying batch fastMNN(combined,batch=c(combined$dataset, combined$condition), subset.row=chosen.hvgs)...
