Bioconductor BSgenome

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BSgenome

updated 9 weeks ago by James W. MacDonald 65k • written 11 weeks ago by Kate • 0

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OrgDb BSgenome

6 months ago • updated 12 weeks ago mat149 ▴ 70

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BSgenome

updated 3 months ago by eviatar.weizman • 0 • written 24 months ago by remerandmaxence ▴ 10

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SNPlocs BSgenome

written 6 months ago by Stevie Pederson • 0

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intron BSgenome.Hsapiens.UCSC.hg38 BSgenome

updated 10 months ago by ATpoint ★ 4.1k • written 10 months ago by Lillian • 0

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BSgenomeForge BSgenome

updated 10 months ago by James W. MacDonald 65k • written 10 months ago by kyliecode • 0

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bsgenome GenomicFeatures package

updated 11 months ago by Hervé Pagès 16k • written 11 months ago by Manish • 0

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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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