Bioconductor Forum

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biostrings Biostrings

updated 30 minutes ago by James W. MacDonald 65k • written 1 hour ago by mat149 ▴ 70

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DESeq2

updated 3 hours ago by Michael Love 41k • written 18 hours ago by HAK • 0

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GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData

updated 4 hours ago by James W. MacDonald 65k • written 16 hours ago by Yveto • 0

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DiffBind

7 hours ago Ian D. ▴ 70

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1.7k

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sgseq rnaseq

updated 14 hours ago by Leonard Goldstein ▴ 200 • written 6.7 years ago by Sylvain Foisy ▴ 80

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187

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CopyNumberPlots HMMcopy CopyNumberVariation

updated 23 hours ago by James W. MacDonald 65k • written 1 day ago by SSSJec • 0

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130

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CAMERA limma

1 day ago • updated 21 hours ago Chris • 0

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1.1k

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limma

11 days ago • updated 14 hours ago Chris • 0

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1.0k

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limma microarray statistics

updated 23 hours ago by XW • 0 • written 7.9 years ago by tati6406 • 0

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1.5k

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limma limma

updated 23 hours ago by XW • 0 • written 13.0 years ago by Babara Mueller ▴ 10

10 results • Page 1 of 1

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Answer: Store output of matchPWM() by James W. MacDonald 65k

Something like this? ``` ind <- as.logical(sapply(hitlist, length)) out <- do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) …

Answer: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k

This has been asked before, but with a multi factor design, the LFC for coefficient X adjust for the others, in a way that is often hard to…

Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by James W. MacDonald 65k

You don't say what array that is, so I will guess. ``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame…

Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200

`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…

Comment: Help with error using camera() in limma by Chris • 0

Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.

Votes

SPIA plotP giving error

Answer: Fold change calculation in Diffbind vs. DESEQ2?

C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB

C: Extremely big genes in annotation TxDb packages

Make custom Txdb class objects from Txdb

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