Bioconductor Metagenome

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deseq2 metagenome mocat

updated 5.3 years ago by Michael Love 43k • written 5.3 years ago by anjali.kumari ▴ 10

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deseq2 metagenome

updated 7.3 years ago by Michael Love 43k • written 7.3 years ago by ghanbari.msc ▴ 10

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geneanswers metagenome kegg

updated 8.5 years ago by Guangchuang Yu ★ 1.2k • written 10.1 years ago by francesca.defilippis ▴ 100

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metagenome normalization metagenomics

8.6 years ago David ▴ 860

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metagenome microbiome metagenomeseq

updated 9.9 years ago by Joseph Nathaniel Paulson ▴ 280 • written 9.9 years ago by jovel_juan ▴ 30

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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40

Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …

Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k

limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k

Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…

Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60

Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k

For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…

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Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio

C: edgeR and lack of counts ID on CPM matrix

A: DESeq2 Following RSEM

A: importing RSEM data into DESeq2

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