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Hi André,
Fortunately, based on your previous advices, scifi pipeline is running. We are getting feature count matrices as output. Is there a way in which we could get UMI-count matrices ? Does sci…
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In the paper, the mean counts are modeled as Y ~ NB(u = pi * exp(XB + log(w) ) , theta), where pi is the number of UMI's in each cell and theta is the dispersion parameter.
Three questions
Is thi…
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Hi,
I am trying to load a umi count matrix to build a seurat object but the problem is that in this count matrix which is seemingly is in a flat file format both the cell ids and gene ids are in ro…
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The first and second step can be run,but when I run follow mode:
**tnode = sct.train.Trainer(atest2)**
such an error can occur:
ValueError Traceback (most recen…
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# Context
@jahilton reported the case in [**#cell-science-platform**](https://czi-sci.slack.com/archives/C06AVGFV222/p1712859564920389).
This issue depends on [Add modality](https://github.com/…
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hi,
Thanks for your great work.:)
I read that log2(TPM+1) data are needed but not UMI gene-barcode matrix from cellranger pipeline of 10x genomics.can UMI count matrix be input by somehow transf…
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Hi, Qian,
I am using adata as input of the h5ad file converted from Seurat. Adding data from RNA as X, adding counts from RNA as raw, transferring meta.data to obs.
During model training, I enc…
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Hi Alex,
I am trying to analyze our customized 10x snRNA-seq data to see alternative splicing, but I found junction read counts stored in `matrix.mtx` do not match my observation of bam files in I…
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I am a bit confused about the "preparation of expression matrices" section in the STAR methods of the optimal transport paper. You define three different expression matrices: the UMI matrix, the log-n…
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A very nice tool! I am dealing with perturbation data without gRNA matrix UMI count matrix (low MOI). Is it correct to manually transform the perturbation status of each cell into a binary gRNA matrix…