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Academia EOF && cat > eGenesis <<
My personal experience giving up on academia to bet on industry
Oct 3, 2019
5 min read
How to set up cellranger to make your hpc admin happy
I found myself to force to use cellranger. Meanwhile it helps a lot to run from bcl files to single cell counts matrixes, I discovered …
Jul 11, 2019
5 min read
How to set up public dataset analysis with bcbio-nextgen
We use bcbio-nextgen for the analysis of sequencing data, mainly, (sc)RNAseq, smallRNAseq, DNASeq and ChIPSeq. It is not rare that we …
Apr 5, 2019
2 min read
Get colors for your heatmap annotation
This post will show how to configure quickly the colors for the annotation of rows/columns that go on top or on the side of a heatmap. …
Sep 21, 2018
5 min read
How to plot miRNA, gene expression and functional analysis together
This post should show you an easy way to get the following data type integrated into a figure: functional enrichment analysis gene …
Aug 12, 2018
4 min read
Subset of object creates bigger RDA file size than original object
This is a funny story, and I will try to tell you how I realized I don’t know anything about R in 400 words. I work at the …
Aug 23, 2017
4 min read
DEGreport to plot nice RNA-seq figures
Differentially gene expression analysis with RNA-seq data is quite common nowadays, and there are pretty good Bioconductor packages for …
Mar 20, 2017
2 min read
miRNA Annotation Tools Comparison
In summary: I will show which is the best miRNA mapping tool. I used several options for this benchmarking: miraligner from SeqBuster …
Mar 24, 2016
3 min read
small RNA abundance [miss-] viz
My PhD was focused on small RNA sequencing data. I had a problem when I wanted to visualized the amount of small RNAs from the …
Oct 29, 2013
2 min read
Lying factor in figures
What is the lying factor in figures? It is the ratio between the difference of two numbers and the difference of the visualization of …
Aug 7, 2013
2 min read
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