Bioconductor Bowtie

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noiseq rsubread tophat bowtie bowtie2

5.5 years ago Marcelo Laia ▴ 450

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4

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Bowtie quasr rnaseq

updated 8.9 years ago by Dario Strbenac ★ 1.5k • written 8.9 years ago by tarek.mohamed ▴ 10

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deseq deseq2 edger tophat bowtie

9.5 years ago ysdel ▴ 40

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4

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r bowtie

updated 9.5 years ago by Sean Davis 21k • written 9.5 years ago by a.afshinfard ▴ 10

4 results • Page 1 of 1

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Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200

Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k

That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k

Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30

Thank you James, that really helped! I tried CODE `enter code here` but I must have dome it incorrectly, as it showed all in red.

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k

Please come back to the support site and view your post - I've fixed it for you. If you want to show people your targets file, just paste t…

Votes

Answer: nightmare to make custom txdb for genomes from ToxoDB

Comment: nightmare to make custom txdb for genomes from ToxoDB

Answer: Normalizing batch effects using technical replicates for DGE analysis between tw

Answer: nightmare to make custom txdb for genomes from ToxoDB

A: Advice on correcting for batch effect using DESeq2

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