Bioconductor Cheminformatics

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Cheminformatics ChemmineR ChemmineDrugs

17 months ago Sean • 0

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cheminf ChemmineOB Cheminformatics ChemmineR

3.4 years ago adelenelai • 0

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bioassayr chemmineR cheminformatics

5.8 years ago Anthony Nash ▴ 20

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831

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limma edger deseq2 cheminformatics

updated 6.4 years ago by Aaron Lun ★ 28k • written 6.4 years ago by perdedorium • 0

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1.4k

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cellhts2 cheminformatics

updated 8.1 years ago by Joseph Barry ▴ 160 • written 8.1 years ago by Andreia Fonseca ▴ 810

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software error R cheminformatics package installation eiR

updated 8.6 years ago by khoran ▴ 10 • written 8.6 years ago by rjrich • 0

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Cheminformatics Visualization Cancer Ovarian DEXSeq minfi DESeq2 BaseSpaceR epivizr minfi

11.5 years ago Martin Morgan 25k

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1.4k

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Metabolomics Cheminformatics Visualization xcms Metabolomics Cheminformatics Visualization

14.9 years ago Gabriella Rustici ▴ 60

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Cheminformatics Clustering Cheminformatics Clustering

16.5 years ago Thomas Girke ★ 1.7k

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1.1k

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Cheminformatics Clustering Cheminformatics Clustering

17.3 years ago Thomas Girke ★ 1.7k

10 results • Page 1 of 1

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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

Here, estimateGLMRobustDisp() was used just to get the diagnostic BCV plot by plotBCV(y). The robust NB dispersions were not used for the D…

Answer: Please, I desperately need help with DESeq2. Three groups of repeated measures w by Michael Love 43k

I have to reserve my time on the support site for software related questions. I recommend working with a local statistician or someone fami…

Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a by Michael Love 43k

I would probably just do the M vs M analysis. You could instead include a term for sex and have a model with all 45 samples, but the M vs M…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0

They provide the code they used for DGE analysis in a gitlab link that can be found in the paper. In there you can find: ```` # estimate d…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

It is not possible to use both. estimateGLMRobustDisp() estimates negative binomial dispersions for each gene, whereas glmQLFit() estimates…

Votes

C: How does edgeR cpm function calculate log(CPM) values?

Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis

scater/scran with TPMs from Salmon - counts?

A: Full length single-cell RNA-seq - tximport output for downstream analysis

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