Bioconductor RNAseq analysis

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deseq2 timecourse multiple factor design RNAseq analysis differential gene expression

updated 7.3 years ago by Gavin Kelly ▴ 690 • written 7.3 years ago by c.nicole ▴ 50

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3.4k

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rnaseq analysis variancestabilizingtransformation normalization cpm edger

updated 6.7 years ago by Wolfgang Huber ★ 13k • written 6.7 years ago by svlachavas ▴ 840

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818

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rnaseq analysis

updated 6.0 years ago by James W. MacDonald 67k • written 6.0 years ago by marak • 0

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2.2k

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filterByExpression edgeR RNAseq analysis edger

updated 4.8 years ago by Gordon Smyth 52k • written 4.8 years ago by hcnbox • 0

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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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Comment: Problems with oarfish + tximport + swish by Michael Love 43k

Great thanks for posting the issue and sticking with it Annaleigh

Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0

Awesome possum! Update works!! Thank you so much for the help and guidance!

Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0

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Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k

> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…

Comment: Problems with oarfish + tximport + swish by Michael Love 43k

Let me see if I can add some code to tximeta to cover this case. I've added an argument `skipRanges` in devel branch which should allow: …

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Answer: Error in download.file for TCGAutils::symbolsToRanges

Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?

Answer: Limma Interaction Effect with Covariates

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