Bioconductor Qiime

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949

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deseq2 R fedora qiime

updated 6.3 years ago by Michael Love 42k • written 6.3 years ago by kperlejewski • 0

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1.6k

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deseq2 R microbiome phyloseq qiime

updated 6.9 years ago by Michael Love 42k • written 6.9 years ago by ssingh59 • 0

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1.1k

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deseq2 qiime

updated 7.1 years ago by Michael Love 42k • written 7.1 years ago by syafiqkamarulazman • 0

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2.5k

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R qiime

updated 7.6 years ago by James W. MacDonald 67k • written 7.6 years ago by trichter • 0

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2.1k

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biom json hdf5 qiime phyloseq

updated 8.0 years ago by Bernd Fischer ▴ 550 • written 8.0 years ago by newmanss • 0

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1.8k

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metagenomeseq qiime biom

updated 8.3 years ago by Joseph Nathaniel Paulson ▴ 280 • written 8.3 years ago by dr.richrodrigues • 0

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20k

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r phyloseq import_biom otu qiime

updated 9.1 years ago by mcmurdie ▴ 20 • written 9.1 years ago by moanam • 0

7 results • Page 1 of 1

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Comment: How many of my genes from my gene list are in each KEGG pathway? by josephasmith1310 • 0

> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…

Comment: EuroBioC2024 abstract submission is open! by Esperan • 0

Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…

Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k

I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…

Comment: Adjusted p-values become NA when sub-setting samples by txema.heredia • 0

Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…

Answer: DESeq2 interaction between cancer cells and microenvironment cells by Michael Love 42k

I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …

Votes

A: p.adjust BH generates duplicate values

Answer: Adjusted p-values become NA when sub-setting samples

Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice

Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim

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

Awards • All

Supporter to Paul Harrison ▴ 100

Popular Question to Mikhail Dozmorov ▴ 30