Bioconductor Rnaseq analysis

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deseq2 timecourse multiple factor design RNAseq analysis differential gene expression

updated 7.4 years ago by Gavin Kelly ▴ 690 • written 7.4 years ago by c.nicole ▴ 50

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3.5k

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rnaseq analysis variancestabilizingtransformation normalization cpm edger

updated 6.8 years ago by Wolfgang Huber ★ 13k • written 6.8 years ago by svlachavas ▴ 840

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2.1k

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limma differential gene expression rnaseq analysis alignment RSEM

updated 7.1 years ago by Aaron Lun ★ 28k • written 7.1 years ago by goldberg.jm ▴ 10

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2.2k

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filterByExpression edgeR RNAseq analysis edger

updated 4.9 years ago by Gordon Smyth 52k • written 4.9 years ago by hcnbox • 0

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829

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rnaseq analysis

updated 6.1 years ago by James W. MacDonald 68k • written 6.1 years ago by marak • 0

5 results • Page 1 of 1

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Comment: accounting for vs. removing batch effects with DESeq2 in RNAseq analysis by Blair • 0

@[Sprunki][1] wrote: Please read the vignette and think about adhering to the author's best practice, which discusses batch impacts. [1…

Comment: error in ChAMP loading file by 81becky • 0

hi Giulia, it sounds like you're facing a frustating issue with your chAMP import. One common suggestion is to double-check your CSV fomat…

Answer: DESeq2 adujsted p-value cutoff seemingly not working by James W. MacDonald 68k

From `?results' ``` On p-values: By default, independent filtering is performed to select a set of genes for multiple tes…

Comment: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = by SofieK • 0

Thank you, I will try this and see.

Comment: DiffBind - question on the use of filtered or unfiltered input data by deltaexploitss • 0

Data input is the adding of data into a computer. This can take place through an input device such as a keyboard. A user inputs data, which…

Votes

Answer: Efficiently working with HDF5-backed SingleCellExperiments

Efficiently working with HDF5-backed SingleCellExperiments

A: Effect of lfcThreshold on p-value in DESeq2

Answer: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet

What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?

Awards • All

Popular Question to Vincent J. Carey, Jr. 6.7k

Teacher to Gordon Smyth 52k

Scholar to James W. MacDonald 68k