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How to cite the GTEx project

October 16, 2017by inesdesantiago Leave a comment

Originally posted on Bits of DNA:
The GTEx consortium has just published a collection of papers in a special issue of Nature that together provide an unprecedented view of the…

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Confusion matrix terminology is taxicab trigonometry

January 3, 2017by inesdesantiago Leave a comment

Originally posted on Bits of DNA:
What are confusion matrices? In the 1904 book Mathematical Contributions to the Theory of Evolution, Karl Pearson introduced the notion of contingency tables. Sometime around the 1950s the…

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How to Use t-SNE Effectively

October 21, 2016by inesdesantiago Leave a comment

t-SNE stands for t-Distributed Stochastic Neighbor Embedding (t-SNE) and is a popular technique for dimensionality reduction. The technique was introduced by van der Maaten and Hinton in 2008. T-SNE is […]

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Your Biomarker doesn’t work (and a case for reproducible research)!

July 13, 2016by inesdesantiago 1 Comment

We have all hear about those “breakthrough biomarkers” that.. simply.. do not work! There have been numerous reports in the literature that investigate why certain biomarkers don’t work after all. […]

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FPKM, TPM, RSEM or RPKM!? QC metrics for RNA-seq quantification

April 27, 2016by inesdesantiago Leave a comment

There are many quantification methods proposed to quantify expression abundance of genes, transcripts, exons or splicing junctions. But we all want to use the best one, right? Rafael A. Irizarry […]

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Too few (or none) differential expressed genes? A way to fix the null hypothesis in DESeq2

January 27, 2016by inesdesantiago Leave a comment

I’ve been using DESeq2 for testing for differential expression between samples. It’s always worked great, but for some datasets it is not working correctly. I have a DESeqResults object called […]

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Computational Reproducibility – Workshop in Cambridge, UK

September 19, 2015by inesdesantiago Leave a comment

“I did this yesterday and it worked!” “I can’t remember which version of this software I used to make this figure” “I can’t reproduce the analysis in this paper” “Why […]

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Top Posts & Pages

  • Should you transform RNA-seq data: Log, VST, voom?
  • How to Use t-SNE Effectively
  • Too few (or none) differential expressed genes? A way to fix the null hypothesis in DESeq2
  • Calculate nucleotide frequency with Rsamtools pileup
  • Essential dplyr cheat sheet for R
  • FPKM, TPM, RSEM or RPKM!? QC metrics for RNA-seq quantification
  • Consistency accross ChIP-seq replicates using non-overlapping windows
  • Tools for quality control of RNA-seq and ChIP-seq data
  • Make R beep at end of script or function! – and what does the fox say?
  • P-values

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Recent Posts

  • How to cite the GTEx project
  • Confusion matrix terminology is taxicab trigonometry
  • How to Use t-SNE Effectively
  • Your Biomarker doesn’t work (and a case for reproducible research)!
  • FPKM, TPM, RSEM or RPKM!? QC metrics for RNA-seq quantification

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opiniomics - has moved! www.opiniomics.org

opiniomics - has moved! www.opiniomics.org

Sequencing QC and data analysis blog

Sequencing Quality Control, statistics and bioinformatics blog

bioinfoblog.it

bioinformatics, human genetics, cancer, and nerdish stuff

Train of Thoughts

An Eye to the World, an Eye to the Net

blog.openhelix.eu

Scientific B-sides

The flipside of the A-side: after-hour ramblings on life, the universe and everything

Next-Gen Sequencing

Sequencing Quality Control, statistics and bioinformatics blog

MassGenomics

Medical genomics in the post-genome era

Genomes Unzipped

Sequencing Quality Control, statistics and bioinformatics blog

GenomeRef

Sequencing Quality Control, statistics and bioinformatics blog

EpiGenie | Epigenetics and Non-Coding RNA News

Epigenetics & Non-Coding RNA News, Reviews, Interviews and Technology

CoreGenomics

Sequencing Quality Control, statistics and bioinformatics blog

Cancer Research UK - Science blog

The latest news, views and opinions from Cancer Research UK

Bits of DNA

Reviews and commentary on computational biology by Lior Pachter

Beatrice the Biologist

Oh, Science. You're Funny.

Bad Science

Sequencing Quality Control, statistics and bioinformatics blog

Sequencing QC and data analysis blog
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