Posts Tagged ‘ek’

BoxPlotR: a web tool for generation of box plots

September 21, 2014

They published a paper on a web tool to generate box plots !! http://www.nature.com/nmeth/journal/v11/n2/full/nmeth.2811.html QT:{{”
Despite the obvious advantages of the box plot for simultaneous representation of data set and statistical parameters, this method is not in common use, in part because few available software tools allow the facile generation of box plots. For example, the standard spreadsheet tool Excel is unable to generate box plots.

M.S. and J.W. conceived of the box plot tool
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Related:
http://bioinformatics.oxfordjournals.org/content/early/2014/01/21/bioinformatics.btu038.abstract

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Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

August 9, 2014

QT:{{”
We discovered abundant (12 to 24%) monoallelic expression of autosomal genes and that expression of the two alleles occurs independently. The monoallelic expression appeared random and dynamic because there was considerable variation among closely related embryonic cells. “}}

‘Kardashian index’ in science

July 30, 2014

A great article discussing the major issue of hyped social media presence:

“Social media makes it very easy for people to build a seemingly impressive persona by essentially ‘shouting louder’ than others. Having an opinion on something does not make one an expert.”

http://genomebiology.com/2014/15/7/424

Looking for a tool to find fusion transcript — use Grep :)

June 28, 2014

The “Grep” Command But Not FusionMap, FusionFinder or ChimeraScan Captures the CIC-DUX4 Fusion Gene from Whole Transcriptome Sequencing Data on a Small Round Cell Tumor with t(4;19)(q35;q13)

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099439

correlations – “stay away from bedsheets”

May 13, 2014

need adjusted p values after multiple hypothesis correction

Spurious Correlations
http://www.tylervigen.com

Twitter data grants

May 11, 2014

https://blog.twitter.com/2014/introducing-twitter-data-grants

And now a video game for cancer genomics !

May 11, 2014

we can play in meetings, and tell people we are working on cancer research.
http://scienceblog.cancerresearchuk.org/2014/02/04/download-our-revolutionary-mobile-game-to-help-speed-up-cancer-research

After TopHat, Bowtie and Cufflinks — here’s Ballgown !

April 6, 2014

“Flexible isoform-level differential expression analysis with Ballgown” http://biorxiv.org/content/early/2014/03/30/003665

Allele-specific expression at single cell resolution

January 19, 2014

QT:{{”
We discovered abundant (12 to 24%) monoallelic expression of autosomal genes and that expression of the two alleles occurs independently. The monoallelic expression appeared random and dynamic because there was considerable variation among closely related embryonic cells. Similar patterns of monoallelic expression were observed in mature cells. Our allelic expression analysis also demonstrates the de novo inactivation of the paternal X chromosome.
“}}

http://www.sciencemag.org/content/343/6167/193.full

Guide to cancer genomics

January 17, 2014

http://www.cancer.gov/cancertopics/understandingcancer/cancergenomics/AllPages