Bioconductor Open

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167

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Biostrings

1 day ago • updated 6 hours ago Ali Osman • 0

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gmapR

1 day ago Tom Lin • 0

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120

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quantro

updated 1 day ago by ATpoint ★ 4.2k • written 2 days ago by Chutian • 0

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104

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Seurat DESeq2 single-cell scRNA Pseudobulk

updated 23 hours ago by Guido Hooiveld ★ 4.0k • written 2 days ago by Sara • 0

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conumee

3 days ago Maximus • 0

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168

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oligo source Install

updated 20 minutes ago by James W. MacDonald 66k • written 4 days ago by Guido Hooiveld ★ 4.0k

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265

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RNASeq Rsubread

updated 4 days ago by Wei Shi ★ 3.6k • written 5 days ago by atan • 0

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Bioconductor dada2

6 days ago • updated 5 days ago abhisek001 • 0

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376

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Cha ChAMP

updated 6 days ago by James W. MacDonald 66k • written 15 days ago by e1271094 • 0

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1.7k

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MethylationEPICv2.0 conumee

updated 1 day ago by sgomez • 0 • written 14 months ago by luca.s ▴ 50

10 results • Page 1 of 1

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Comment: Cannot install oligo on Fedora by James W. MacDonald 66k

I think the solution is for the C code in `oligo` to be updated to work with more modern versions of `zlib`. The `zlibbioc` package is real…

Comment: Error in gseDO function by Guido Hooiveld ★ 4.0k

I don't fully understand what you are asking... Yet, in my opinion it doesn't make sense to use the results of only 12 genes for ORA (nor G…

Comment: Counter-directional LFC shrinkage by ATpoint ★ 4.2k

Is this RNA-seq? The unshrunken MA-plot looks very odd and indicates that normalization is completely offset.

Answer: ChAMP not available for bioconductor 3.19 by shepherl 3.9k

See https://support.bioconductor.org/p/9158324/#9158336 . We have reached out to goseq to fix the package; we have a community member …

Answer: Counter-directional LFC shrinkage by Michael Love 42k

It's not just the average count but also the dispersion that affects apeglm. You can try ashr for another type of shrinkage.

Votes

A: DESeq2: add annotations (from data frame) to DESeqDataSet

Answer: Error in gseDO function

Comment: what the test method for enrichGO in clusterProfiler?

A: Comparison between two different group's pathway analysis results

DiffBind Batch Effect

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