Bioconductor Timecourse

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154

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DESeq2 timecourse DifferentialExpression

updated 26 days ago by James W. MacDonald 65k • written 26 days ago by joshua.mannheimer • 0

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1.4k

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deseq2 timecourse design and contrast matrix

updated 7 weeks ago by ta_awwad ▴ 10 • written 8.5 years ago by Assa Yeroslaviz ★ 1.5k

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241

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DESeq2 timecourse time

updated 3 months ago by Michael Love 41k • written 3 months ago by Anastasiia • 0

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265

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RNASeq DESeq2 timecourse

3 months ago WS • 0

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2.7k

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limma edger timecourse without replicate voom

written 7.5 years ago by Camila Orellana ▴ 10

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909

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time-series DESeq2 RNASeq timecoursedata TimeCourse

updated 8 months ago by ATpoint ★ 4.1k • written 8 months ago by Debebe • 0

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1.3k

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Transcriptomics TimeCourse DESeq2

updated 9 months ago by Michael Love 41k • written 10 months ago by smac97 • 0

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506

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timecoursedata RNASeqData TimeCourse DESeq2

updated 9 months ago by Michael Love 41k • written 9 months ago by georgii.vdovin • 0

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559

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timecourse KEGG DESeq2

updated 11 months ago by Michael Love 41k • written 11 months ago by Fred • 0

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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.

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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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