Bioconductor Workflow

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Bioconductor Workflow

updated 3.0 years ago by Gordon Smyth 52k • written 3.0 years ago by sarastew1994 • 0

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ExperimentData Deprecation Software Release Workflow

3.2 years ago • updated 2.7 years ago shepherl 4.1k

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Workflow Software ExperimentData Deprecation

4.0 years ago • updated 3.6 years ago shepherl 4.1k

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976

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Software annotation experiment workflow

updated 4.4 years ago by shepherl 4.1k • written 4.4 years ago by gnanaprakash.s • 0

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948

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rnaseqGene workflow deseq2

updated 5.0 years ago by Michael Love 43k • written 5.0 years ago by Assa Yeroslaviz ★ 1.5k

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software error deseq2 workflow rnaseqGene

updated 5.5 years ago by Martin Morgan 25k • written 5.5 years ago by pavan-bioconductor • 0

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RNA-Seq Workflow

updated 5.6 years ago by Gordon Smyth 52k • written 5.6 years ago by detroit.drive • 0

7 results • Page 1 of 1

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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…

Votes

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

A: Expected counts from RSEM in DESeq2

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