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As a novice in genomic data analysis, one of my goal is to benchmark how well a clustering method works. I ran across this practice of doing k-means at R-exercises the other day and felt it might be a nice start because k-means is easy to perform and conceptually simple for me to correlate what is happening behind the clustering machinery.

Ritchie, ME, Phipson, B, Wu, D, Hu, Y, Law, CW, Shi, W, and Smyth, GK (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies.Nucleic Acids Research 43(7), e47.

Original Article: Jha, S. et al. Trans-kingdom mimicry underlies ribosome customization by a poxvirus kinase. Nature 546,651–655 (2017). This is a story about how poxvirus turns human translation machinery in favor of viral transcript by modifying a ribosome-associated gene, RACK1.

Recently, I analyzed a few single cell RNA-seq datasets and experimented with several new tools from recent publication. While it was fun, most datasets were just too large for my poor laptop to process, and I relied a lot on our server.

Original article: Li, H. et al. Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-Cell RNA Sequencing. Cell 171,1206.e22–1207 (2017). The complexity of the nervous system has fascinated scientists for centries.

Hello there. I had not anticipated to encounter this problem again so soon, but I did when I was installing yet another package on my own laptop. ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.

After a while of playing around, I’ll say the best way to use R with a Notebook-style interface on a server where you are no superuser would be using Anaconda, and then run R inside Anaconda to get whatever package you need.

No Longer That “Next” Generation When I was doing my undergraduate project, microarray was like black magic that turned the labyrinth of gene expression into colorful heatmap and brought your paper into top-notch journals.