Bioconductor Tcga

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GDCRNATools TCGA

6 days ago glaciya2018 • 0

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223

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TCGAbiolinks TCGA clinical TCGA-BRCA

written 7 weeks ago by BioinfoMug • 0

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168

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TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data

9 weeks ago BioinfoMug • 0

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illimina 450k methylation qsea MEDIPS TCGA

updated 3 months ago by Matthias Lienhard ▴ 240 • written 7.1 years ago by justinburgener ▴ 20

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recount3 TCGA RNASeq

updated 5 months ago by Leonardo Collado Torres ★ 1.0k • written 6 months ago by tangming2005 ▴ 190

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503

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TCGA GenomicDataCommons GDC

written 10 months ago by António Miguel de Jesus Domingues ▴ 510

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BatchEffect TCGA WGCNA

updated 10 months ago by ATpoint ★ 4.1k • written 10 months ago by khaserdene99 • 0

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DESeq2 recount GTEx TCGA recount3

updated 12 months ago by ATpoint ★ 4.1k • written 12 months ago by David ▴ 20

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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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