Bioconductor Spike-in

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deseq2 ruvseq spike-in time course time series

updated 7.1 years ago by davide risso ▴ 980 • written 7.1 years ago by staceyborrego ▴ 20

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3.3k

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Spike-in RNASeqR DESeq2 Normalization rna-seq

updated 16 months ago by manuel.fernandez • 0 • written 2.8 years ago by cicely.day • 0

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2.6k

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deseq2 Tximport Sizefactors normalizationfactors spike-in

updated 4.6 years ago by Michael Love 43k • written 4.6 years ago by Hina Bandukwala • 0

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2.1k

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deseq2 apeglm rna-seq spike-in

updated 4.4 years ago by Michael Love 43k • written 4.4 years ago by nadezda.fursova ▴ 10

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1.3k

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scran spike-in

6.8 years ago • updated 6.7 years ago supremerulersuraj • 0

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Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Michael Love 43k

hi, for questions about what statistical analysis approach to use, I recommend you work with a local statistician or someone familiar with …

Comment: Problems with oarfish + tximport + swish by Michael Love 43k

I'm not certain that this will work with Oarfish, the documentation only mentions Salmon and piscem. I'd use tximport for now.

Answer: Problems with oarfish + tximport + swish by Michael Love 43k

> This is fine Did tximeta() print that a matching transcriptome was found?

Answer: DESeq2 Heatmap by swbarnes2 ★ 1.4k

> However, I've been asked why the first column (vehicle/control) isn't > entirely zero on the log fold change (logFC) expression scale. …

Comment: Biomart and ensembl not working? by James W. MacDonald 67k

``` > library(biomaRt) > mart <- useEnsembl("ensembl","hsapiens_gene_ensembl") Ensembl site unresponsive, trying useast mirror > mart Objec…

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Answer: Limma Interaction Effect with Covariates

Comment: DESeq2 for single cell pseudobulk processing

C: Limma: how to get same output as topTable but for all the genes ?

A: Processing agilent data by limma

A: Linear regression in DESeq2

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Commentator to Michael Love 43k