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tidyverse R SingleCellExperiment SingleCellData

written 2.1 years ago by Sitapriya • 0

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edgeR R tidyverse tidybulk

3.2 years ago Amit Indap ▴ 10

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Rscript tidyr dataframe tidyverse offtopic

updated 3.4 years ago by Marcel Ramos 700 • written 3.4 years ago by Nikhil • 0

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bioconductor R tidyverse IlluminaHumanMethylationEPICanno.ilm10b4.hg19.

updated 7.4 years ago by James W. MacDonald 68k • written 7.4 years ago by jonellevillar • 0

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variantannotation tidyverse genomicfeatures

updated 8.4 years ago by Hervé Pagès 16k • written 8.4 years ago by yduan004 ▴ 20

5 results • Page 1 of 1

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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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