Bioconductor Rnaseq analysis

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deseq2 timecourse multiple factor design RNAseq analysis differential gene expression

updated 7.5 years ago by Gavin Kelly ▴ 690 • written 7.5 years ago by c.nicole ▴ 50

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rnaseq analysis variancestabilizingtransformation normalization cpm edger

updated 6.8 years ago by Wolfgang Huber ★ 13k • written 6.9 years ago by svlachavas ▴ 840

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852

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rnaseq analysis

updated 6.2 years ago by James W. MacDonald 68k • written 6.2 years ago by marak • 0

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filterByExpression edgeR RNAseq analysis edger

updated 5.0 years ago by Gordon Smyth 52k • written 5.0 years ago by hcnbox • 0

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2.3k

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limma differential gene expression rnaseq analysis alignment RSEM

updated 7.2 years ago by Aaron Lun ★ 28k • written 7.2 years ago by goldberg.jm ▴ 10

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Answer: affy::rma results doesn't match with ncbi website by ATpoint ★ 4.7k

Exact OMCIS reproduction down to the values without code and software version is borderline impossible. Either use the values as provided o…

Answer: Use of org.Rn.eg.db with GRCr8 reference genome by James W. MacDonald 68k

You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…

Comment: DESeq2 swap ensembl gene id rownames with gene symbol column by Erika • 0

Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…

Answer: Clarification on GOALL / GO2ALLORFs mapping by James W. MacDonald 68k

It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…

Comment: Can't post a question? by DavideSant • 0

Thank you, this was super useful!

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Comment: Can't post a question?

Answer: Limma - Complex 2-way multi-level contrast with paired samples

Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks

Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression

Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf

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