Bioconductor Dnastring

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DNAString

updated 6.9 years ago by Hervé Pagès 16k • written 6.9 years ago by pgreenbank • 0

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biostrings subsetting View dnastring dnaseq

updated 8.6 years ago by James W. MacDonald 65k • written 8.6 years ago by arado1 • 0

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dnastring

updated 8.8 years ago by James W. MacDonald 65k • written 8.8 years ago by eulerphi8 • 0

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Biostrings DNAString Rcpp

updated 20 months ago by Hervé Pagès 16k • written 2.0 years ago by James • 0

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Answer: DESEQ2 output gives multiple groups when only 2 groups are present by ATpoint ★ 4.0k

In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …

Answer: A ComBat-seq issue: the covariates are confounded by ATpoint ★ 4.0k

```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…

Comment: DESeq2 setting significant p-value by Dev • 0

after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …

Comment: DESeq filtering specific to contrasts by Carlin95 • 0

But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…

Comment: Reading huge bismark coverage files using bbseq::read.bismark by jacques.imbert • 0

Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.

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Comment: Reading huge bismark coverage files using bbseq::read.bismark

Answer: Reading huge bismark coverage files using bbseq::read.bismark

Answer: How many of my genes from my gene list are in each KEGG pathway?

Comment: Light difference when using coef vs omit a group when compare 3 groups.

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