Bioconductor Qiime

Showing : qiime • reset

votes

726

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deseq2 R fedora qiime

updated 5.4 years ago by Michael Love 41k • written 5.4 years ago by kperlejewski • 0

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1.2k

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deseq2 R microbiome phyloseq qiime

updated 6.0 years ago by Michael Love 41k • written 6.0 years ago by ssingh59 • 0

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replies

908

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deseq2 qiime

updated 6.2 years ago by Michael Love 41k • written 6.2 years ago by syafiqkamarulazman • 0

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2.2k

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R qiime

updated 6.7 years ago by James W. MacDonald 64k • written 6.7 years ago by trichter • 0

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1.8k

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biom json hdf5 qiime phyloseq

updated 7.1 years ago by Bernd Fischer ▴ 550 • written 7.1 years ago by newmanss • 0

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1.4k

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metagenomeseq qiime biom

updated 7.3 years ago by Joseph Nathaniel Paulson ▴ 280 • written 7.3 years ago by dr.richrodrigues • 0

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19k

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r phyloseq import_biom otu qiime

updated 8.2 years ago by mcmurdie ▴ 20 • written 8.2 years ago by moanam • 0

7 results • Page 1 of 1

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Answer: What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE) by James W. MacDonald 64k

There are two types of probes used by Illumina. The type I probes bind directly to the CpG site and have two different probes (one for a me…

Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance by Michael Love 41k

Then for the remaining genes that you don't think are DE, just plot like this: ``` dds_sub <- dds[,dds$condition %in% c("x","y")] dropleve…

Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance by samer • 0

yes i turned it off @mikelove

Answer: autonomics: example("read_somascan", package = "autonomics") fails, but not on B by Mike Smith ★ 6.2k

It looks like `autonomics` uses `BiocFileCache` to create a local copy of the data and save repeat downloading. Given the (relatively) rec…

Answer: Small RNA-seq Analysis DESEQ2 : Unexpected Significance by Michael Love 41k

I notice you are using `betaPrior=TRUE`. We have set to default and recommended `betaPrior=FALSE` for many years (since version 1.16 in 201…

Votes

Answer: WGCNA documentation not available

Comment: Can the limma package be applied to Log2 RUV-normalized data?

Answer: Correct the batch effect in methylation analysis in R

Comment: Why is DMRcate not available for Bioconductor version 3.18?

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Popular Question to Assa Yeroslaviz ★ 1.5k

Scholar to Gordon Smyth 49k

Popular Question to Lluís Revilla Sancho ▴ 720

Popular Question to Frederik Ziebell ▴ 20