Bioconductor Batchqc

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982

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BatchQC BatchEffect rnaseqGene Normalization

updated 20 months ago by jessica.anderson ▴ 10 • written 21 months ago by Đình Vinh • 0

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1.1k

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BatchQC BatchEffect RNASeq

updated 20 months ago by jessica.anderson ▴ 10 • written 21 months ago by ttt • 0

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1.8k

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BatchQC batchinDeseq2. columnsincolData.

21 months ago Galina • 0

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2.9k

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BatchQC RNASeqData sva BatchEffect

updated 2.6 years ago by ATpoint ★ 5.0k • written 2.6 years ago by amnahsiddiqa ▴ 10

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1.6k

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TCGAbiolinks BatchQC BatchEffect

updated 2.5 years ago by wrab425 • 0 • written 2.9 years ago by snijesh ▴ 200

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1.5k

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BatchQC

updated 5.0 years ago by Malcolm Cook ★ 1.6k • written 5.0 years ago by Josh • 0

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BatchQC RNA-seq R Shiny batch-effect

5.8 years ago manninm • 0

7 results • Page 1 of 1

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Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k

I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…

Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k

Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…

Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0

Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…

Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0

Hello, I was also wondering about the same issue. Did you figure it out?

Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0

FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…

Votes

Answer: Subsetting data verses contrasts [DESeq2]?

A: WGCNA differences two groups 10 replicates each group

A: WGCNA sample size minimum: why?

Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name

Answer: Can you colour dendrogram branch clusters in pheatmap?

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Popular Question to Peter Hickey ▴ 760