Bioconductor Gene set enrichment

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gsva plage differential expression gene set enrichment

6.0 years ago krassowski.michal ▴ 40

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1.7k

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camera limma gene set analysis gene set enrichment

updated 6.1 years ago by Gordon Smyth 52k • written 6.1 years ago by emeline.perthame • 0

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1.2k

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gene set analysis gene set enrichment limma

updated 6.2 years ago by Gordon Smyth 52k • written 6.2 years ago by jaynishshah • 0

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1.3k

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gene set enrichment KEGG

updated 6.8 years ago by Lluís Revilla Sancho ▴ 760 • written 6.8 years ago by RMRG ▴ 10

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2.1k

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limma edger barcodeplot gene set enrichment mroast

updated 6.9 years ago by Gordon Smyth 52k • written 6.9 years ago by srmaruyama • 0

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3.5k

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limma goana gene set enrichment

7.1 years ago emy_66 • 0

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4.0k

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DOSE clusterprofiler annotation gene ontology gene set enrichment

updated 7.1 years ago by Guangchuang Yu ★ 1.2k • written 7.1 years ago by kirannbishwa01 ▴ 20

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1.4k

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gene ontology go analysis gene set enrichment gene set analysis News

updated 7.4 years ago by Martin Morgan 25k • written 7.4 years ago by triZZla • 0

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2.8k

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limma camera gene set analysis gene set enrichment

updated 7.8 years ago by Gordon Smyth 52k • written 7.9 years ago by natalia.pietrosemoli • 0

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2.9k

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topgo gene ontology gene set enrichment rna-seq bioinformatics

updated 7.9 years ago by Lluís Revilla Sancho ▴ 760 • written 8.2 years ago by fromhj304 ▴ 10

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2.6k

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rna-seq bioinformatics gene ontology gene set enrichment go

updated 8.2 years ago by Guangchuang Yu ★ 1.2k • written 8.2 years ago by fromhj304 ▴ 10

11 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

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

A: Using RSEM reads for DESeq2

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