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DESeq2 multifactorial nested

updated 13 months ago by Basti ▴ 770 • written 13 months ago by jd • 0

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nested DESeq2

updated 2.2 years ago by Michael Love 41k • written 2.3 years ago by yampolsk • 0

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deseq2 Phyloseq Nested

updated 4.1 years ago by Michael Love 41k • written 4.1 years ago by mpuli011 • 0

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deseq2 Paired Nested

updated 4.3 years ago by Michael Love 41k • written 4.3 years ago by julia.chariker ▴ 10

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deseq2 nested de

updated 4.4 years ago by Michael Love 41k • written 4.4 years ago by gaio.transposon • 0

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edgeR nested glm glmQLFit

updated 5.0 years ago by Aaron Lun ★ 28k • written 5.0 years ago by jcalis ▴ 10

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edger nested design matrix differential expression

updated 9.2 years ago by Aaron Lun ★ 28k • written 9.2 years ago by Mauve • 0

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edger nested estimatedispersions

9.2 years ago Mauve • 0

8 results • Page 1 of 1

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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.

Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100

See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…

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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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