Bioconductor Single-cell RNA-seq

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single-cell RNA-seq scran normalization

updated 3.8 years ago by Aaron Lun ★ 28k • written 3.8 years ago by daniel.borshagovski • 0

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Cancer Genomics Cancer Epigenomics Single-cell RNA-Seq Network theory Job

updated 4.2 years ago by ronniepubg • 0 • written 4.3 years ago by Andrew Teschendorff ▴ 60

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Comment: SummarizedExperiment is now warning on attach about `read_block` namespace confl by Hervé Pagès 16k

Available since last Friday. See https://bioconductor.org/packages/3.17/DelayedArray

Comment: Diffbind "No genome detected" by James W. MacDonald 63k

The error you see comes from an internal function called `pv.genome` that inspects the header of your BAM file and tries to infer the genom…

Comment: Diffbind "No genome detected" by kyliecode • 0

Hi James, Thanks for your reply! For the blacklist, I just used the one provided by DiffBind, which is "DBA_BLACKLIST_MM10". For the grey…

Answer: DESeq2 on multilevel design variable by ATpoint ★ 2.9k

You can make your life simply and use a contrast for each, for example: ```r library(DESeq2) dds <- makeExampleDESeqDataSet() diagnosis <…

Answer: Diffbind "No genome detected" by James W. MacDonald 63k

You can specify the greylist in the same manner as the blacklist, which should fix your problem.

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Teacher to James W. MacDonald 63k