Bioconductor Autoplot

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ggcyto ggcyto_arrange autoplot

updated 3.4 years ago by Jake Wagner ▴ 310 • written 3.4 years ago by alavy ▴ 30

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ggbio ideogram autoplot

4.8 years ago gpwhiz ▴ 10

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ggcyto autoplot axis

5.7 years ago anders.tondell ▴ 30

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ggbio autoplot

updated 7.4 years ago by James W. MacDonald 63k • written 7.4 years ago by Lescai, Francesco ▴ 380

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ggbio autoplot color vignette

updated 7.7 years ago by aaron ▴ 10 • written 7.7 years ago by timothypyork • 0

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ggbio ggplot2 autoplot bioconductor gene models

updated 7.7 years ago by snf • 0 • written 7.7 years ago by danhovelson ▴ 10

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ggbio bugs tracks autoplot

8.7 years ago • updated 8.6 years ago cooketho • 0

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Comment: DataFrame Construction With Non-standard Column by Hervé Pagès 16k

SimpleList is a List derivative and List derivatives in general don't need protection. For example, a GRangesList object (which is also a L…

Answer: Deseq2, how to model design for comparing Mutant mouse at age 14 days versus Mu by swbarnes2 ★ 1.3k

The Status grouping you show above is good to use if you want to simply compare one subset of samples to another subset. The ~Genotype +…

Answer: Remove duplicates of colData in TreeSummarizedExperiment by Michael Love 40k

Copying my code from Slack for posterity. James' code is more streamlined for this step I think. ``` # make a dataset that has duplicate s…

Comment: DataFrame Construction With Non-standard Column by James W. MacDonald 63k

Oh, ok. I understand. Technically both should work according to what the help page for `DataFrame` says (both `SimpleList` and `list` have …

Comment: DeSeq2 design fails (full model matrix is less than full rank) by Basti ▴ 720

As recommended, you can only perform ~group. You can use contrasts do perform the comparison AA5 vs FHIN1 (see [DESeq2 vignette][1]), but t…

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Answer: Further analysis after limma regression output

A: collapseReplicates in DESeq2

Answer: DataFrame Construction With Non-standard Column

Steps needed to change design (relevel factors) in DESeq2

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