Bioconductor Bowtie

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noiseq rsubread tophat bowtie bowtie2

6.4 years ago Marcelo Laia ▴ 450

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Bowtie quasr rnaseq

updated 9.8 years ago by Dario Strbenac ★ 1.6k • written 9.8 years ago by tarek.mohamed ▴ 10

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deseq deseq2 edger tophat bowtie

10.4 years ago ysdel ▴ 40

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r bowtie

updated 10.4 years ago by Sean Davis 21k • written 10.4 years ago by a.afshinfard ▴ 10

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Answer: Error installing Seqinfo by fabio.marroni • 0

I am answering my own question. I found the solution thanks to [this post][1], and I am writing here the very simple procedure: 1) Instal…

Comment: Getting a large intercept with DESeq2 by Michael Love 43k

Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…

Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k

As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…

Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k

The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …

Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k

There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…

Votes

Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors

Issues with downloading biomaRt - SeqInfo and S4 Vectors

Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors

Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif

Using edgeR or DESeq2 to analyze allele-specific expression?

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