Showing : ggplot • reset
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ggplot and geom_lines for clustering
ggplot
updated 5 months ago by ▴ 80 • written 6 months ago by • 0
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205
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Using a clustree object to draw a "classical" dendogram
ggplot dendogram ggtreeExtra clustree ggtree
6 months ago christian.dina • 0
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381
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TCseq plot
TCseq ggplot
15 months ago jochen • 0
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1.4k
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How to solve Error in ggplot could not find function "+<-"?
ggplot
21 months ago nattzy94 ▴ 20
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434
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problem regarding bioconducter package installation
ggplot
updated 2.4 years ago by 3.8k • written 2.4 years ago by • 0
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544
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How to plot "chromosomewise" "allele frequency" of a "Hybrid" in comparison to its "Inbred parents"
ggplot2 ggplot cmplot
4.5 years ago gens8094 • 0
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0
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528
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How to plot "chromosomewise" "allele frequency" of a "Hybrid" in comparison to its "Inbred parents"
ggplot cmplot ggplot2
4.5 years ago gens8094 • 0
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20k
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Error in .External.graphics(C_layout, num.rows, num.cols, mat, as.integer(num.figures)
edger ggplot
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 10
2
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1
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1.5k
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Error in plot.new() : figure margins too large
edger ggplot
updated 6.0 years ago by 48k • written 6.0 years ago by ▴ 10
1
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1
reply
1.3k
views
ggplot same data, different plots
ggplot2 ggplot plot
updated 7.7 years ago by 63k • written 7.7 years ago by ▴ 50
10 results • Page 1 of 1
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Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta by Michael Love 40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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