ALRA
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KlugerLab
Imputation method for scRNA-seq based on low-rank approximation
I am working with a particularly large dataset consisting of 2,423,133 cells and 1,091 genes. Using the ALRA, I ran into repeated warnings about integer overflow. Here’s the warning: r$>...
I am working on a project to compare multiple samples. Is it better to run ALRA on each sample individually or to merge them all together and then run ALRA...
I'm working with a matrix of over 200,000 cells and 36,000 genes. "I first tried the 'RunALRA' function in Seurat. Then, I extracted the expression table, converted it into a...
Hey ALRA team, I would like to ask alra's performance on very large data sets（～600k cell) I am using scapy pipeline and I have 2 quertions: 1. I noticed that...
Hi @linqiaozhi The alra.low.memory function has a line checking whether the input A_norm is of class matrix but the output of class(A_norm) is actually a vector with multiple elements e.g....
I am working with a matrix that has 53201 cells and 20245 genes. Its size in memory is only 482 MB as a dgCMatrix but 8.62 GB as.matrix(). When I...
Hello, as the title say, can I use the imputed matrix to find marker genes and differentially expressed genes for downstream analysis ?
hi, I imputed my dataset with alra in seurat. after the imputation I integrated the alra assay and calculated pca, umap and clusters. the problem is that when I look...
Dear all, I am kind of lost how to deal with the results of ALRA. When I process a Seurat object with ALRA I get a new assay. How do...
Hello Developers and Maintainers!! @mojaveazure @rcannood @JunZhao1990 @inoue0426 @linqiaozhi I ran into an issue while trying to use `ALRAChooseKPlot` function as follows: ```r > Assays(t) [1] "RNA" "integrated" > DefaultAssay(t)...
