Bioconductor Annotatepeak

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GRanges ChIPseeker annotatePeak TxDb EnsDb

updated 5.8 years ago by Johannes Rainer ★ 2.1k • written 5.8 years ago by foehn ▴ 100

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chipseeker annotatepeak

updated 7.1 years ago by Guangchuang Yu ★ 1.2k • written 7.1 years ago by Wojeff • 0

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genomicranges granges iranges annotatepeak

updated 8.6 years ago by Michael Lawrence ★ 11k • written 8.6 years ago by Dimitris Polychronopoulos ▴ 80

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annotatePeak chipseeker chipseq org.Mm.eg.db TxDb.Mmusculus.UCSC.mm9.knownGene

updated 9.1 years ago by Martin Morgan 25k • written 9.3 years ago by Elsa • 0

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Answer: Epic v2 Annotation CpG_maf source? by James W. MacDonald 67k

Those all come from dbSNP by way of UCSC. [See here][1], particularly lines 114 and onward. Here is no MAF for a CpG. The MAF is for the…

Comment: Deseq2 res Function by James W. MacDonald 67k

In addition to Mike's comment, do note that if you are generating a heatmap based on the set of significant genes, the direction of your co…

Answer: Struggle with the replicates of epic array data by James W. MacDonald 67k

You shouldn't be using beta values for a linear model that assumes a unimodal, untruncated distribution (beta values are strictly on (0-1) …

Comment: Identifying potentially associated gene set to drug response using GSVA by Robert Castelo ★ 3.4k

So, if I understand correctly, you derived GSVA scores from gene sets corresponding somehow to drugs in your RNA-seq data. Since GSVA score…

Answer: Deseq2 res Function by Michael Love 43k

> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…

Votes

Appropriate use of the function treat of the limma package

Comment: Is it recommended to analyze different tissues together when using edgeR

Answer: Deseq2 res Function

Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification

Answer: ANOVA like approach of edgeR

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