Bioconductor Htseq

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553

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DEXSeq HTSeq R

8 months ago • updated 7 months ago yr542 • 0

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1.0k

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DESeq2 microRNA HTSeq

16 months ago abhay.kanodia • 0

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707

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DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount

updated 17 months ago by Michael Love 41k • written 17 months ago by abhay.kanodia • 0

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701

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DESeq2 htseq DEGseq RNASeq read

updated 18 months ago by Michael Love 41k • written 18 months ago by CP • 0

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1.1k

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software error HTSeq installation

updated 4.2 years ago by Martin Morgan 25k • written 4.2 years ago by eric33150 • 0

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4.4k

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voom htseq edgeR limma RNASeq123

updated 5.3 years ago by Gordon Smyth 50k • written 6.9 years ago by wd ▴ 30

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1.5k

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DEXSeq dexseq_count htseq

7.2 years ago mat.lesche ▴ 90

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1.9k

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HTSeq HTSeqCounts Could not find function DEXSeq

updated 8.0 years ago by Martin Morgan 25k • written 8.0 years ago by sakura.nussbaum ▴ 10

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Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k

I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …

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…

Votes

Answer: DEseq2 coefficient

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

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Scholar to Rory Stark ★ 5.2k

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