Bioconductor Qiime

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971

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deseq2 R fedora qiime

updated 6.4 years ago by Michael Love 43k • written 6.4 years ago by kperlejewski • 0

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1.6k

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deseq2 R microbiome phyloseq qiime

updated 7.1 years ago by Michael Love 43k • written 7.1 years ago by ssingh59 • 0

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1.2k

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deseq2 qiime

updated 7.3 years ago by Michael Love 43k • written 7.3 years ago by syafiqkamarulazman • 0

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2.5k

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R qiime

updated 7.8 years ago by James W. MacDonald 67k • written 7.8 years ago by trichter • 0

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2.2k

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biom json hdf5 qiime phyloseq

updated 8.2 years ago by Bernd Fischer ▴ 550 • written 8.2 years ago by newmanss • 0

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1.8k

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metagenomeseq qiime biom

updated 8.4 years ago by Joseph Nathaniel Paulson ▴ 280 • written 8.4 years ago by dr.richrodrigues • 0

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20k

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r phyloseq import_biom otu qiime

updated 9.2 years ago by mcmurdie ▴ 20 • written 9.2 years ago by moanam • 0

7 results • Page 1 of 1

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Comment: Mean variance curve troubleshoot filtering by gingergeiger22 • 0

Gordon, thank for your response. 'filterByExpr()' was marginally better. I can see high variability in samples within the groups from the M…

Comment: What is the importance of `--countReadPairs` in featureCounts on paired end data by rohitsatyam102 ▴ 20

Since I don't know which organism you are working on, I would recommend using the following: `-s 0` if library is unstranded `-C` Discard…

Comment: What is the importance of `--countReadPairs` in featureCounts on paired end data by rohitsatyam102 ▴ 20

Yes use this option. It is recommended for PE and if you don't use it you will observe nearly twice the number of counts in your results. H…

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

I edited the previous post. I meant to remove the estimateGLMRobustDisp line in the second snipper : ```` DGE_list_object <- estimateGLMR…

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

Sorry, I had forgotten estimateGLMDisp() produces weights as well as NB dispersions. The weights from estimatGLMRobustDisp() were intended …

Votes

Comment: Comparing different method for DESEQ2

Answer: How do I fix an odd voom plot in a combined dataset?

Comment: How do I fix an odd voom plot in a combined dataset?

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

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