Bioconductor Tcgautils

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625

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normalization RNASEQ Normalization TCGAutils TCGA

updated 17 months ago by ATpoint ★ 4.1k • written 17 months ago by Deniz • 0

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1.8k

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MultiAssayExperiment curatedTCGAData TCGAutils

3.4 years ago svlachavas ▴ 830

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1.2k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 3.4 years ago by Marcel Ramos 690 • written 3.4 years ago by svlachavas ▴ 830

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1.3k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 3.4 years ago by Marcel Ramos 690 • written 3.5 years ago by svlachavas ▴ 830

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3.9k

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TCGAutils TCGAbiolinks GenomicDataCommons

updated 4.8 years ago by Marcel Ramos 690 • written 4.8 years ago by Dario Strbenac ★ 1.5k

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766

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TCGAutils

updated 5.1 years ago by Levi Waldron ★ 1.1k • written 5.1 years ago by vittorio.fortino • 0

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1.3k

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TCGAutils multiassayexperiment coad

updated 5.8 years ago by Marcel Ramos 690 • written 5.8 years ago by mario.zanfardino ▴ 160

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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.

Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0

Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.

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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