Bioconductor Scran

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scoreMarkers scran

updated 10 months ago by Peter Hickey ▴ 740 • written 10 months ago by Assa Yeroslaviz ★ 1.5k

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smart-seq2 scRNAseq scran

11 months ago • updated 10 months ago Lluís Revilla Sancho ▴ 730

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229

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scran bluster scater scuttle

updated 5 weeks ago by ATpoint ★ 4.1k • written 5 weeks ago by Dario Strbenac ★ 1.5k

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scRNAseq quickcluster scRNA scran

4 months ago ruba-mahmoud • 0

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134

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scran BiocParallel bluster

7 days ago • updated 6 days ago ATpoint ★ 4.1k

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819

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scran SingleCellExperiment

10 months ago Lluís Revilla Sancho ▴ 730

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429

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BiocParallel scran

updated 3 months ago by ATpoint ★ 4.1k • written 3 months ago by qwang178 • 0

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354

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scran

updated 8 months ago by ATpoint ★ 4.1k • written 8 months ago by Maximilian • 0

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Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k

But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…

Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0

Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…

Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k

Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…

Comment: Store output of matchPWM() by James W. MacDonald 65k

Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…

Comment: DEseq2 coefficient by JKim • 0

Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…

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SPIA plotP giving error

Answer: Fold change calculation in Diffbind vs. DESEQ2?

C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB

C: Extremely big genes in annotation TxDb packages

Make custom Txdb class objects from Txdb

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