Bioconductor GenomicScores

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txdbmaker GenomicScores phastCons100way.UCSC.hg38 GenomicFeatures

updated 4 hours ago by James W. MacDonald 67k • written 2 days ago by rania.alanany • 0

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1.5k

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GenomicScores

updated 2.2 years ago by Robert Castelo ★ 3.4k • written 2.4 years ago by Robert • 0

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2.7k

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GenomicScores MafH5.gnomAD.v3.1.1.GRCh38

updated 2.4 years ago by Robert Castelo ★ 3.4k • written 2.6 years ago by Robert • 0

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1.7k

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GenomicScores

updated 3.1 years ago by Robert Castelo ★ 3.4k • written 3.2 years ago by nattzy94 ▴ 20

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3.8k

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genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer

updated 2 days ago by rania.alanany • 0 • written 4.7 years ago by Biologist ▴ 120

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Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela by James W. MacDonald 67k

The 'voom transformed counts' are just logCPM with a prior count of 0.5. The 'magic' of limma-voom is the weights that are computed and the…

Comment: Limma Interaction Effect with Covariates by kitzhu • 0

Thanks so much, James!

Answer: Limma Interaction Effect with Covariates by James W. MacDonald 67k

The second way is how you should do it.

Answer: Using Affymetrix Custom Array by James W. MacDonald 67k

To use `gcrma` you need to have the probe sequences for that array. It doesn't appear that ArrayExpress has the probe sequences, and I don'…

Answer: Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178 by James W. MacDonald 67k

Those are both HuGene-2.0 ST arrays, so there should be no differences. If you are getting the CEL files, it's a simple process to annotate…

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Dotplot from enricher outputting very few genes

Answer: [How to construct a model.matrix ]

C: DESeq2 baseMean values for each sample

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