Bioconductor Parameters

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xcms adjustRtime parameters scantime error biocparallel error

6.3 years ago abrsoule ▴ 30

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1.7k

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MAST AIC calcuation Parameters single cell hurdle model

updated 22 months ago by rproendo ▴ 30 • written 6.9 years ago by mcalgaro93 • 0

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1.7k

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rtracklayer liftOver parameters minMatch

updated 7.8 years ago by Michael Lawrence ★ 11k • written 7.8 years ago by Nik dAK ▴ 10

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2.0k

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Volcano plot Parameters

updated 8.3 years ago by Gordon Smyth 53k • written 8.3 years ago by Sanches • 0

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1.4k

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lpsymphony R parameters control warm start

updated 9.6 years ago by Wolfgang Huber ★ 13k • written 9.6 years ago by chiel • 0

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Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0

Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …

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 ▴ 20

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…

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Answer: Clarification on counting in Rsubread (featureCounts)

Comment: Clarification on counting in Rsubread (featureCounts)

C: ControlGenes/ housekeeping genes Deseq2

Answer: Clarification on counting in Rsubread (featureCounts)

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

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Great Question to fl ▴ 20

Popular Question to Lluís Revilla Sancho ▴ 760