Bioconductor Bowtie

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noiseq rsubread tophat bowtie bowtie2

6.7 years ago Marcelo Laia ▴ 450

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Bowtie quasr rnaseq

updated 10.1 years ago by Dario Strbenac ★ 1.6k • written 10.1 years ago by tarek.mohamed ▴ 10

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deseq deseq2 edger tophat bowtie

10.7 years ago ysdel ▴ 40

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r bowtie

updated 10.7 years ago by Sean Davis 21k • written 10.7 years ago by a.afshinfard ▴ 10

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Comment: Subsetting DDS object for individual conditions over time by A ▴ 60

Hi @atpoint Thank you for the quick reply! and this makes sense! I will confirm with a corr to see how the SFs differ but also how DE dif…

Answer: Subsetting DDS object for individual conditions over time by ATpoint ★ 5.0k

It would surprise my quite a bit if the size factors would differ notably between subset or not. I would always try to keep the size factor…

Comment: GSEA error by Adithi • 0

Thank you so much. That makes perfect sense to me. I will work on this.

Comment: tximeta cannot open annotation gtf? by Michael Love 43k

Yes, so this is the same type of error you would get if you tried to assemble a *SummarizedExperiment* manually with tximport + GTF process…

Answer: tximeta cannot open annotation gtf? by ATpoint ★ 5.0k

> Timeout of 60 seconds was reached You have to increase the default timeout limits for downloads, `options(timeout=3600)`. GENCODE serve…

Votes

Answer: RNA Seq using Lrt

Answer: DESeq2 LRT Reduced Formula

Answer: DESeq2: LRT or WALD guidance

Answer: GSEA error

Answer: OrgDb for maize

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