Showing : single-cell RNA-seq • reset
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scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
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Job: JOB: Research Associate in Computational / Statistical Epigenomics and Single-Cell Omics
Cancer Genomics Cancer Epigenomics Single-cell RNA-Seq Network theory Job
updated 5.7 years ago by • 0 • written 5.7 years ago by ▴ 60
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Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by Paul • 0
Unfortunately I've updated my code with the newest GRCm39 genome, and yet I am still getting the same error.... Is there anything else I ca…
Comment: WGCNA with TPM tables by ATpoint ★ 4.5k
WGCNA is not a Bioconductor package, but generally: If you want to do serious analysis then find the raw data. There is no guarantee what …
Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by James W. MacDonald 67k
The `EnsDb.Mmusculus.v79` package is mm38, not mm39. If you want a current `EnsDb`, use `AnnotationHub` ``` > library(AnnotationHub) >…
Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k
I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…
Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 880
If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …
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Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Comment: does anyone how to create rarefaction curves from a phyloseq object?
Answer: ANOVA like approach of edgeR
A: ANOVA-like test with edgeR
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
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