Bioconductor Scuttle

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7.0k

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scran scater scuttle

updated 4.3 years ago by Aaron Lun ★ 28k • written 4.3 years ago by enricoferrero ▴ 660

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2.9k

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scran SingleCellExperiment scuttle scater

updated 3.9 years ago by Aaron Lun ★ 28k • written 3.9 years ago by enricoferrero ▴ 660

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2.0k

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scater SingleCellExperiment BiocParallel scuttle scran

3.1 years ago enricoferrero ▴ 660

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1.6k

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normalizeCounts scran librarySizeFactors scuttle scRNAseq

2.8 years ago behr201 • 0

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534

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scran bluster scater scuttle

updated 8 months ago by ATpoint ★ 4.6k • written 8 months ago by Dario Strbenac ★ 1.5k

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1.9k

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scuttle scater seurat SpatialExperiment

22 months ago cathalgking ▴ 10

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938

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scuttle scater SpatialExperiment

updated 22 months ago by alan.ocallaghan ▴ 160 • written 23 months ago by cathalgking ▴ 10

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1.6k

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scuttle scater

updated 15 months ago by ATpoint ★ 4.6k • written 15 months ago by Abbi Edwards • 0

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scuttle

updated 4 hours ago by Aaron Lun ★ 28k • written 12 hours ago by Adam • 0

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Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k

You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…

Comment: contrast matrix design for a continuous variable by dtzhu337 • 0

Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…

Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k

Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …

Comment: fail to use addPerROIQC in Rmd by liu.n • 0

That's odd. So it can run successfully within markdown but would be failed when knitting?

Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0

> dim(spe) [1] 19962 425

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Answer: contrast matrix design for a continuous variable

A: What's the difference between p.adjust and qvalue?

Answer: DESeq2- merging technical vs biological replicates

Comment: What type of counts data to import for performing Isoform analysis in edgeR

Answer: What type of counts data to import for performing Isoform analysis in edgeR

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