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Deseq2 rlog or 'regular' normalization?
Deseq2 rlog transformation data visualization
7.4 years ago sunil.mangalam • 0
4
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3
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362
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RNA-Seq analysis with DESeq2: showing two conditions do *not* significantly differ
deseq2 RNA-Seq uniform distribution data visualization
updated 2.9 years ago by 13k • written 2.9 years ago by • 0
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Pathview: visualization of data
pathview data visualization
updated 6.9 years ago by ★ 1.6k • written 6.9 years ago by ★ 3.5k
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Using pathview with uncommon species leads to Errors
pathview Kegg rnaseq data visualization
updated 6.5 years ago by ★ 1.6k • written 6.5 years ago by • 0
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2.1k
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Input file of NGS data for Pathview
rnaseq pathview data visualization
updated 7.3 years ago by ★ 1.6k • written 7.3 years ago by ▴ 10
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1
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489
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DNA Deferential metheylation
data visualization
6.1 years ago tarek_2050 • 0
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624
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Visualize FlowSet by Date
FlowSet data visualization cellcounts
5.6 years ago Maria • 0
1
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0
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783
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Job: Summer Vacation Studentships in Data Science, MRC Cancer Unit, University of Cambridge, UK
data science data visualization machine learning cancer Job
4.8 years ago • updated 4.7 years ago Shamith.Samarajiwa ▴ 180
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how to construct mds plot of differentially expressed genes?
differentially expressed genes mds plot data visualization
3.8 years ago pratikshasharma47 • 0
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1.3k
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Job: Multiple postdoctoral fellowships are available immediately in the Gehlenborg Lab in the Department of Biomedical Informatics at Harvard Medical Scho…
bioinformatics bioinformatician job data visualization Job
7.3 years ago Doe, Aimee ▴ 40
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Answer: collapseReplicates error after tximeta by Michael Love 39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2? by Michael Love 39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by Michael Love 39k
Specifying `controlGenes` means it estimates the size factors over those rows. But size factors when used later as offsets in GLM or when u…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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