Bioconductor Spike-in

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Spike-in RNASeqR DESeq2 Normalization rna-seq

updated 2.0 years ago by manuel.fernandez • 0 • written 3.4 years ago by cicely.day • 0

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deseq2 apeglm rna-seq spike-in

updated 5.1 years ago by Michael Love 43k • written 5.1 years ago by nadezda.fursova ▴ 10

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deseq2 Tximport Sizefactors normalizationfactors spike-in

updated 5.2 years ago by Michael Love 43k • written 5.2 years ago by Hina Bandukwala • 0

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scran spike-in

7.5 years ago • updated 7.4 years ago supremerulersuraj • 0

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4.1k

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deseq2 ruvseq spike-in time course time series

updated 7.7 years ago by davide risso ▴ 980 • written 7.7 years ago by staceyborrego ▴ 20

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Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200

I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …

Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k

Not sure I understand. You ask how to do something and then show how one would do so.

Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10

Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…

Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200

I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …

Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k

Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…

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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?

Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea

Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi

Can NanoString data be analyzed using DESeq2?

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Popular Question to Robert Castelo ★ 3.4k