Bioconductor SubSeq

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r expressionset subseq rnaseq

updated 8.3 years ago by Martin Morgan 25k • written 8.3 years ago by rrcutler ▴ 70

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subseq Xvector dnastringset

updated 7.4 years ago by Hervé Pagès 16k • written 7.4 years ago by Sophie • 0

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biostrings subseq

updated 7.7 years ago by Martin Morgan 25k • written 7.7 years ago by tobias.kockmann ▴ 20

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subSeq rarefaction

3.7 years ago Jirapat • 0

4 results • Page 1 of 1

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Comment: Using Normalized Counts in DESeq2 by Michael Love 42k

Also, just to add, there are many dozens of posts on this topic of DESeq2 applied to TCGA counts, normalized or other. Recommend google sea…

Answer: Using Normalized Counts in DESeq2 by ATpoint ★ 4.5k

TCGA raw counts can be obtained for example using the TCGAbiolinks or recount packages.

Comment: How to reverse complement some elements of a DNAStringSet by Christine Jones • 0

Fantastic, thank you

Comment: When running contrasts, does it use normalized read counts? by Katherine • 0

Ok, so the comment I was given where they said DeSeq2 should be with normalized counts is incorrect. the ```normalized_counts``` variable …

Answer: How to reverse complement some elements of a DNAStringSet by James W. MacDonald 67k

You should always try the vectorized method first, rather than looping. ``` > myFasta[myFasta_rc] <- reverseComplement(myFasta[myFasta_…

Votes

Answer: When running contrasts, does it use normalized read counts?

Comment: featureCounts fails to load annotation file

Answer: How to reverse complement some elements of a DNAStringSet

Answer: KEGGgraph result difference

Answer: What should be the normalization protocol for RNA seq data for WGCNA?

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