Bioconductor Ribosome profiling

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deseq2 differential translation ribosome profiling

updated 5.2 years ago by Michael Love 43k • written 5.2 years ago by katerinadouka91 • 0

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1.5k

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aligning ribosome profiling RNA-Seq

5.3 years ago Crispy • 0

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1.5k

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deseq2 ribosome profiling wald lrt

updated 6.0 years ago by Michael Love 43k • written 6.0 years ago by indrik.wijaya ▴ 20

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2.5k

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deseq2 sequencing ribosome profiling riboseq multiple factor design

updated 6.4 years ago by Michael Love 43k • written 6.4 years ago by kotcha.m ▴ 10

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3.3k

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deseq2 ribosome profiling

updated 6.5 years ago by Michael Love 43k • written 6.5 years ago by xiaozhuo ▴ 10

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1.3k

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R riboseqr ribosome profiling

6.9 years ago bsad • 0

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861

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riboprofiling ribosome profiling

7.3 years ago nicholsonangela7 • 0

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2.2k

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biomart bioconductor grangeslist cds ribosome profiling

updated 7.6 years ago by Hervé Pagès 16k • written 7.6 years ago by Walter F. Baumann ▴ 10

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2.5k

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deseq2 translation efficiency spikes ribosome profiling

8.2 years ago GFM ▴ 20

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1.8k

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riboseqr ribosome profiling

updated 8.8 years ago by Thomas J Hardcastle ▴ 180 • written 8.9 years ago by alper.celik • 0

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1.7k

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R riboseqr ribosome profiling

9.2 years ago ohtack9 • 0

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2.4k

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deseq2 linear model ribosome profiling stats

updated 9.4 years ago by Ryan C. Thompson ★ 7.9k • written 9.4 years ago by Jake ▴ 90

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Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k

Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0

But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…

Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0

After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```

Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k

R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…

Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0

Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…

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A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor

A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio

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