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219

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scran bluster scater scuttle

updated 4 weeks ago by ATpoint ★ 4.0k • written 4 weeks ago by Dario Strbenac ★ 1.5k

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scuttle scater

updated 7 months ago by ATpoint ★ 4.0k • written 7 months ago by Abbi Edwards • 0

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scuttle scater seurat SpatialExperiment

14 months ago cathalgking ▴ 10

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642

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scuttle scater SpatialExperiment

updated 15 months ago by alan.ocallaghan ▴ 160 • written 15 months ago by cathalgking ▴ 10

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normalizeCounts scran librarySizeFactors scuttle scRNAseq

2.2 years ago behr201 • 0

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scater SingleCellExperiment BiocParallel scuttle scran

2.5 years ago enricoferrero ▴ 660

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scran SingleCellExperiment scuttle scater

updated 3.3 years ago by Aaron Lun ★ 28k • written 3.3 years ago by enricoferrero ▴ 660

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scran scater scuttle

updated 3.7 years ago by Aaron Lun ★ 28k • written 3.7 years ago by enricoferrero ▴ 660

8 results • Page 1 of 1

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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0

Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…

Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k

IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…

Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0

I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…

Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0

Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …

Votes

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Answer: Interpret plot from DiffBind

Answer: How to retrieve gene ontology GO class from gene list?

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Supporter to JKim • 0