Bioconductor RNAseq analysis

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2.1k

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filterByExpression edgeR RNAseq analysis edger

updated 4.7 years ago by Gordon Smyth 51k • written 4.7 years ago by hcnbox • 0

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791

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rnaseq analysis

updated 5.9 years ago by James W. MacDonald 67k • written 5.9 years ago by marak • 0

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3.3k

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rnaseq analysis variancestabilizingtransformation normalization cpm edger

updated 6.5 years ago by Wolfgang Huber ★ 13k • written 6.5 years ago by svlachavas ▴ 830

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limma differential gene expression rnaseq analysis alignment RSEM

updated 6.9 years ago by Aaron Lun ★ 28k • written 6.9 years ago by goldberg.jm ▴ 10

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4.1k

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deseq2 timecourse multiple factor design RNAseq analysis differential gene expression

updated 7.1 years ago by Gavin Kelly ▴ 690 • written 7.1 years ago by c.nicole ▴ 50

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Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0

Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…

Comment: Merge Replicates vs Mixed Model by abadgerw • 0

@gabrielhoffman any insight?

Comment: makeContrastsDream for Interaction by abadgerw • 0

@gabrielhoffman any insight?

Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta by Michael Love 42k

That is the rows that did converge.

Answer: Is my time course analysis with DESeq2 valid? by Michael Love 42k

For choosing the correct statistical design, I recommend working with a local statistician or someone familiar with linear models in R. I h…

Votes

A: Some questions for remove batch effect by using mnnCorrect

A: Recommendations for combining multiple 10x runs into one SingleCellExperiment

Answer: [How to construct a model.matrix ]

Answer: Handling biological replicates in DESeq2

Comment: biomaRt rnorvegicus_gene_ensembl not available anymore

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