Bioconductor Repitools

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repitools promoter tss annotation

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repitools bioconductor cpgDensityCalc

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Baymeth methylation MBD-seq Repitools

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repitools

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BSgenome BSgenome Repitools BSgenome BSgenome Repitools

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BSgenome BSgenome Repitools BSgenome BSgenome Repitools

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GO Repitools GO Repitools

updated 10.4 years ago by Dario Strbenac ★ 1.5k • written 10.5 years ago by Tim Smith ★ 1.1k

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limma Repitools limma Repitools

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Alignment convert Repitools Alignment convert Repitools

updated 5 months ago by Marge • 0 • written 11.3 years ago by José Luis Lavín ▴ 280

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BSgenome BSgenome Repitools BSgenome BSgenome Repitools

updated 12.5 years ago by Chao-Jen Wong ▴ 580 • written 12.5 years ago by Guest User ★ 13k

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Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k

But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…

Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0

Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…

Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k

Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…

Comment: Store output of matchPWM() by James W. MacDonald 65k

Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…

Comment: DEseq2 coefficient by JKim • 0

Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…

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SPIA plotP giving error

Answer: Fold change calculation in Diffbind vs. DESEQ2?

C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB

C: Extremely big genes in annotation TxDb packages

Make custom Txdb class objects from Txdb

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