Bioconductor Qiime

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821

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deseq2 R fedora qiime

updated 5.7 years ago by Michael Love 41k • written 5.7 years ago by kperlejewski • 0

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1.4k

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deseq2 R microbiome phyloseq qiime

updated 6.4 years ago by Michael Love 41k • written 6.4 years ago by ssingh59 • 0

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replies

994

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deseq2 qiime

updated 6.6 years ago by Michael Love 41k • written 6.6 years ago by syafiqkamarulazman • 0

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2.3k

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R qiime

updated 7.1 years ago by James W. MacDonald 65k • written 7.1 years ago by trichter • 0

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1.9k

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biom json hdf5 qiime phyloseq

updated 7.5 years ago by Bernd Fischer ▴ 550 • written 7.5 years ago by newmanss • 0

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1.6k

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metagenomeseq qiime biom

updated 7.7 years ago by Joseph Nathaniel Paulson ▴ 280 • written 7.7 years ago by dr.richrodrigues • 0

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20k

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r phyloseq import_biom otu qiime

updated 8.5 years ago by mcmurdie ▴ 20 • written 8.5 years ago by moanam • 0

7 results • Page 1 of 1

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Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k

Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…

Answer: ATACseq merge peaks by ATpoint ★ 4.0k

That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…

Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10

Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…

Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k

I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…

Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k

Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…

Votes

Comment: Deseq2. decontXcounts not integers. Useful alternative?

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)

biomaRt error: database disk image is malformed

Comment: biomaRt : No lock file for BiocFileCache

Answer: Cross-species analysis - how to compute the mid parent value?

Awards • All

Popular Question to James W. MacDonald 65k

Scholar to Michael Love 41k

Supporter to JKim • 0