February 10 - 14 notes

2014-02-10

R

Guide to deploying shiny on Amazon EC2

Set up alpha account for shinyapps and deployed my ApRxN app!

Followed this guide

Cool R script to query a website and plot Olymic medal data.

ApTranscriptome

Regarding Don’s suggestion to give drop-down list of GO IDs rather than a search box, may be able to use this function that describes relations among GO terms to extract the correct transcripts for a given GO term.

Writing manuscript…

2014-02-11

Reading

Fu, G.K., Xu, W., Wilhelmy, J., Mindrinos, M.N., Davis, R.W., Xiao, W. & Fodor, S.P.A. (2014). Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations. Proceedings of the National Academy of Sciences, 111, 1891–1896.

awesomely massive barcoding of individual cDNA transcripts
sampling of transcripts saturates at about 20x coverage (starting with 10 pg RNA)
“Any transcripts that were present in the starting material at less than 1,000 copies are simply lost”

Li, Y., Cheng, R., Spokas, K.A., Palmer, A.A. & Borevitz, J.O. (2014). Genetic Variation for Life History Sensitivity to Seasonal Warming in Arabidopsis thaliana. Genetics, 196, 569–577.

identify QTL for flowering time (FT) sensitivity to overwintering conditions
phenotypic prediction: BLUPs of QTL effects could predict flowering in 2055 conditions using data from first three environments with r2=0.95

shinyapps error message:

The application unexpectedly exited.

Diagnostic information has been dumped to the JavaScript error console.

2013-02-12

Working on transcriptome manuscript.

Changed shinyapp to “medium” size (up to 500MB RAM) and it now seems to run with problem.

2014-02-13

Working an analysis and manuscript.

2014-02-14

out sick