Bioconductor MSIGDB

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210

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msigdb gmt GSEA

written 5 weeks ago by Georg • 0

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166

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geneset GeneSetEnrichment msigdb

24 days ago • updated 23 days ago Seongsu • 0

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4.0k

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clusterprofiler GSEA MSIGDB

updated 6.1 years ago by Guangchuang Yu ★ 1.2k • written 6.1 years ago by thomasjenner333 • 0

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1.4k

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limma romer msigdb

updated 8.7 years ago by James W. MacDonald 65k • written 8.7 years ago by Jon Manning ▴ 40

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1.2k

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msigdb GSEABase GSVA

updated 2.1 years ago by Robert Castelo ★ 3.3k • written 2.1 years ago by forlani.luca • 0

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1.9k

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gseabase msigdb genesetcollection Tutorial

written 5.8 years ago by t.kuilman ▴ 170

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595

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ssgsea GSVA biotype proteincoding msigdb

updated 4 months ago by Robert Castelo ★ 3.3k • written 4 months ago by snijesh ▴ 20

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1.3k

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category gostats msigdb hypergeometric test

8.7 years ago petyuk ▴ 70

8 results • Page 1 of 1

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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350

Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre

Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k

Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…

Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0

Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…

Votes

Answer: Cross-species analysis - how to compute the mid parent value?

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0