Articles by Matt.0

My newyeaRs resolution: slimming down (Seurat)

January 15, 2020 | Matt.0

I’m currently developing a single-cell RNA Sequencing pipeline for NetworkAnalyst; an open source, web-based platform for comprehensive gene expression profiling & meta-analysis. The website uses mostly R code (via {RServe}???? ), Java for the he...
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How to Choose the Best Open Source Software

March 21, 2019 | Matt.0

Photo by Pankaj Patel on UnsplashAfter reading the O’Reilly book “Foundations for Architecting Data Solutions”, by Ted Malaska and Jonathan Seidman, I reflected on how I chose software/tools/solutions in the past and how I should choose them going forward. As a bioinformatician you need to be able ...
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Web Scraping Google Sheets with RSelenium

January 28, 2019 | Matt.0

Photo by on UnsplashI love to learn new things and one of ways I learn best is by doing. Also it’s been said that you never fully understand a topic until you are able to explain it , I think blogging is a low barrier to explaining things. ...
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10 Tips for Choosing the Optimal Number of Clusters

January 27, 2019 | Matt.0

Photo by Pakata Goh on UnsplashClustering is one of the most common unsupervised machine learning problems. Similarity between observations is defined using some inter-observation distance measures or correlation-based distance measures. There are 5 classes of clustering methods: + Hierarchical Clustering+ Partitioning Methods (k-means, PAM, CLARA)+ Density-Based Clustering+ Model-based Clustering+ Fuzzy Clustering My ...
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Great post Yash!

December 10, 2018 | Matt.0

Great post Yash! For those readers interested in getting data from the fitbit API using R I’ve documented the process here:
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How to Highlight 3D Brain Regions

October 31, 2018 | Matt.0

Recently, I was reading Howard et. al., (2018) “Genome-wide meta-analysis of depression in 807,553 individuals identifies 102 independent variants with replication in a further 1,507,153 individuals” and saw a really cool 3D visualization of highlighted brain regions associated with depression: Source: an exhaustive search I couldn’t find any ...
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Great post!

August 16, 2018 | Matt.0

Great post!I wanted to mention that although many previous studies have used the area under receiver operating characteristic curve (auROC) statistic to benchmark the precision, it misleads evaluators when the test data is (highly) imbalanced see: PLOS...
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Hi Pawel, I’m glad you enjoyed it.

July 25, 2018 | Matt.0

Hi Pawel, I’m glad you enjoyed it. I was trying to play around with facet_grid() earlier but I guess I didn’t stumble upon the proper parameters. Your suggestion works perfectly; not only does it keep each grid x-axis width proportional to its length, but it also keeps ...
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