Showing : qiime • reset
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DESeq2 intstallation error on fedora
deseq2 R fedora qiime
updated 3.8 years ago by 37k • written 3.8 years ago by • 0
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814
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Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 4.5 years ago by 37k • written 4.5 years ago by • 0
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632
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QIIME Differential abundance on multiple studies
deseq2 qiime
updated 4.6 years ago by 37k • written 4.6 years ago by • 0
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1.8k
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QIIME, R and bioconducter
R qiime
updated 5.2 years ago by 59k • written 5.2 years ago by • 0
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phyloseq biom json format conversion needed to hdf5 format for qiime
biom json hdf5 qiime phyloseq
updated 5.6 years ago by ▴ 550 • written 5.6 years ago by • 0
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Metagenome seq errors using biom (1.3) file
metagenomeseq qiime biom
updated 5.8 years ago by ▴ 280 • written 5.8 years ago by • 0
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Error in file(con, “r”) : cannot open the connection
r phyloseq import_biom otu qiime
updated 6.6 years ago by ▴ 20 • written 6.6 years ago by • 0
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Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
Ok.. thanks for your valuable suggestion and quick replies. I have generated an MA plot using plotMASwish. thanks ekta
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by Michael Love 37k
Sorry, I haven't seen this. Maybe try filtering low count genes? ``` keep <- rowSums(counts(dds) >= 10) >= X dds <- dds[keep,] # then run …
Comment: Transcript-level differential expression using DESeq2 by Michael Love 37k
To show some extent of the DTE you can plot the LFC of the significant set and their mean count, we have `plotMASwish` to do this. Another…
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
No, the Volcano plot is not essential. I just wanted to show DETs with the help of a plot. Could you suggest a way for it? What are the oth…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Hi Michael, I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
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Comment: Transcript-level differential expression using DESeq2
Comment: Transcript-level differential expression using DESeq2
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
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