Bioconductor Filterbyexpr

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3.6k

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edgeR DESeq2 filterByExpr

written 8 months ago by caroline.zanchi ▴ 10

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1.7k

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DEG edgeR limma voom filterByExpr

updated 2.1 years ago by Gordon Smyth 53k • written 2.1 years ago by annikagable • 0

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2.4k

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filtering RNA-Seq CPM edgeR filterByExpr

updated 2.6 years ago by Gordon Smyth 53k • written 2.6 years ago by mohammedtoufiq91 ▴ 10

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3.6k

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CPM filterByExpr edgeR design model.matrix

2.8 years ago mohammedtoufiq91 ▴ 10

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3.6k

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CPM filterByExpr edgeR histogram rowsums

3.1 years ago mohammedtoufiq91 ▴ 10

5 results • Page 1 of 1

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Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k

Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …

Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 10

You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…

Comment: Incosistencies in buildSNNGraph() function by ATpoint ★ 5.0k

Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…

Answer: Incosistencies in buildSNNGraph() function by Aaron Lun ★ 29k

The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…

Comment: Opportunity to host EuroBioC2026 Preconference workshops! by TikTsokaas33ocissalpc • 0

Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…

Votes

Answer: Clarification on counting in Rsubread (featureCounts)

C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results

A: Conversion from counts to FPKM

Answer: Incosistencies in buildSNNGraph() function

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Great Question to fl ▴ 20

Popular Question to Lluís Revilla Sancho ▴ 760