Bioconductor Tximport

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2.8k

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salmon edgeR tximport nf-core gene_counts

updated 9 months ago by i.atanasoai • 0 • written 23 months ago by mohammedtoufiq91 ▴ 10

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256

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fishpond tximport tximeta

updated 7 hours ago by Michael Love 43k • written 1 day ago by brown.annaleigh • 0

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3.2k

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edgeR tximport differential expression

updated 17 days ago by Gordon Smyth 52k • written 4.7 years ago by hollandademello ▴ 20

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10k

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bioconductor tximport rnaseq R

updated 10 months ago by Eva • 0 • written 8.3 years ago by ctl • 0

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2.0k

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DESeq2 tximport counts Salmon

updated 10 months ago by Michael Love 43k • written 2.1 years ago by kiqbal • 0

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675

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tximportData summarizeToGene tximport DESeq2 salmon

10 weeks ago LuciaNhu • 0

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629

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tximportData tximport salmon

7 months ago JG13 • 0

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1.8k

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DESeq2 tximport

written 2.2 years ago by L ▴ 50

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441

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tximport

updated 4 months ago by Michael Love 43k • written 4 months ago by rodongo • 0

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950

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tximport tximportData

updated 11 months ago by Matteo • 0 • written 19 months ago by barrypraveen • 0

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2.3k

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tximport deseq2 STAR

updated 7 months ago by rodrigo.duarte88 ▴ 40 • written 5.2 years ago by mohamedrefaat.1.1992 • 0

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473

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tximport DESeq2 GSVA

5 weeks ago georgii.vdovin • 0

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822

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DESeq2 tximport

5 months ago grothmn • 0

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619

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tximport

updated 9 months ago by Michael Love 43k • written 9 months ago by SG • 0

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579

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tximport edgeR Normalization

9 months ago Marianna ▴ 20

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412

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tximport DESeq2

updated 3 months ago by Michael Love 43k • written 3 months ago by oguzhankaraosmanoglu • 0

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530

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DESeq2 tximport

updated 10 months ago by ATpoint ★ 4.6k • written 10 months ago by hemantcnaik • 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: …

Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by Jonathan ▴ 10

Thank you; I was indeed using `DGEList` on the count matrix, but with the multiple edits of the post I forgot to include this step. BTW, …

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

The other reason for doing this is because when you do `topTable(fit)`, you will automatically annotate the output data.

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

If you have versioned Ensembl Gene IDs, you can always use "GENEIDVERSION" for the `select` statement, or just strip off the version number…

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

Answer: Limma Interaction Effect with Covariates

Comment: DESeq2 for single cell pseudobulk processing

C: Limma: how to get same output as topTable but for all the genes ?

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