Bioconductor RLE

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RLE normalization deseq2

updated 22 months ago by ATpoint ★ 4.6k • written 22 months ago by SH ▴ 10

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S4 Rcpp InteractionSet IRanges Rle

updated 4.6 years ago by Aaron Lun ★ 28k • written 4.6 years ago by lklei001 • 0

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deseq2 RLE

updated 5.0 years ago by Michael Love 43k • written 5.0 years ago by f_pardow • 0

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variantannotation VRanges R Rle

updated 6.6 years ago by Valerie Obenchain ★ 6.8k • written 6.6 years ago by Jayendra Shinde • 0

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1.2k

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iranges s4vectors rle rlelist

6.6 years ago endrebak85 ▴ 40

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rle deseq2 normalization

updated 6.7 years ago by Michael Love 43k • written 6.7 years ago by Aurora ▴ 20

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Rle Big data coverageByTranscript

6.8 years ago hauken_heyken ▴ 80

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delayedarray rlelist rle

updated 7.2 years ago by Peter Hickey ▴ 750 • written 7.2 years ago by davide risso ▴ 980

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DataFrame Rle generic expression table

updated 19 months ago by Hervé Pagès 16k • written 7.7 years ago by Charles Plessy ▴ 180

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Rle granges iranges

8.3 years ago my4 ▴ 10

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granges Rle coverage View mean

updated 8.6 years ago by Michael Lawrence ★ 11k • written 8.6 years ago by Christian Ruckert ▴ 170

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biostrings coverage rle iranges

8.7 years ago likeeatingpizza ▴ 10

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rle normalization table

updated 9.3 years ago by Steve Lianoglou ★ 13k • written 9.3 years ago by aiko • 0

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RLE GenomicFeatures rnaseq

updated 9.8 years ago by Hervé Pagès 16k • written 9.8 years ago by gen ▴ 30

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3.0k

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RLE iranges granges coverage

updated 9.8 years ago by Martin Morgan 25k • written 9.8 years ago by gen ▴ 30

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2.2k

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rle list irange grangeslist

updated 9.8 years ago by Chris Seidel ▴ 80 • written 9.8 years ago by gen ▴ 30

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rle Views

9.9 years ago Sean Davis 21k

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views iranges rle

10.0 years ago Janet Young ▴ 740

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affyPLM RLE NUSE

updated 10.0 years ago by Sean Davis 21k • written 10.0 years ago by beverly893 ▴ 10

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1.3k

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Rle boxplot

10.0 years ago Johannes Rainer ★ 2.1k

20 results • Page 1 of 1

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Answer: Selection of correct coefficients or contrasts in DESeq2 by swbarnes2 ★ 1.4k

I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…

Comment: Csaw normalization strategies - general inquiry by Luca • 0

Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …

Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by Quang NN ▴ 10

Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …

Answer: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k

The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…

Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by ATpoint ★ 4.6k

My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …

Votes

Answer: Csaw normalization strategies - general inquiry

A: DESeq2 interaction term

Comment: Recount3 data correspond to TCGA data

Answer: DESeq2- merging technical vs biological replicates

Answer: SingleCellExperiment convenience function for metadata+expression?

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