Bioconductor Msigdb

Showing : msigdb • reset

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708

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GSEABase fgsea msigdb GeneSetEnrichment

3 months ago Assa Yeroslaviz ★ 1.5k

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305

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msigdb fgsea msig

6 months ago Tanvi • 0

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582

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geneset GeneSetEnrichment msigdb

8 months ago Seongsu • 0

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693

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msigdb gmt GSEA

written 9 months ago by Georg • 0

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2.3k

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ssgsea GSVA biotype proteincoding msigdb

updated 12 weeks ago by Ginny • 0 • written 12 months ago by snijesh ▴ 200

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1.8k

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msigdb GSEABase GSVA

updated 2.7 years ago by Robert Castelo ★ 3.4k • written 2.7 years ago by forlani.luca • 0

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2.2k

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gseabase msigdb genesetcollection Tutorial

written 6.5 years ago by t.kuilman ▴ 170

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4.7k

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clusterprofiler GSEA MSIGDB

updated 6.8 years ago by Guangchuang Yu ★ 1.2k • written 6.8 years ago by thomasjenner333 • 0

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1.5k

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limma romer msigdb

updated 9.3 years ago by James W. MacDonald 67k • written 9.3 years ago by Jon Manning ▴ 40

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1.5k

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category gostats msigdb hypergeometric test

9.4 years ago petyuk ▴ 70

10 results • Page 1 of 1

Recent ...

Replies

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…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0

Thanks for your reply!

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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