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docker BiocManager BiocVersion

updated 5.0 years ago by Martin Morgan 25k • written 5.0 years ago by Michael Steinbaugh ▴ 90

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BiocVersion

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BiocVersion

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BiocVersion phangorn ShinyApps

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BiocVersion OrgDb clusterProfiler

17 months ago MK • 0

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destiny BiocVersion

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massgeek Reactome Proteomics STRINGdb

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bioconductoroversight community BiocVersion news

updated 3.1 years ago by aedin • 0 • written 3.2 years ago by Matthew Ritchie ▴ 1000

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BioCor bioc BiocVersion

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bioconductoroversight news community BiocVersion

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Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0

Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…

Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by sredemption • 0

Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)

Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0

Thank you for your reply and I know there is another post similar to this you had mentioned this. How are the genes that I mentioned in the…

Answer: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240

The genes are automatically ordered within `fgsea`, there is no need to sort them manually.

Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k

Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.

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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output

Comment: DEXSeq DEXSeqDataSet count matrix duplication

Comment: Error in champ.load(): The following specified files do not exist

Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos

Using GRanges and IRanges to simply get all chromosome data

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