Posts Tagged ‘from’
GPS4CAM
August 29, 2015Isp-fellows another privacy tool
August 28, 2015Browse More Privately With the Privacy Badger
Jason B. Jones looks at a new plug-in from the Electronic Frontier Foundation that blocks companies from tracking your behavior across multiple sites.
http://chronicle.com/blogs/profhacker/browse-more-privately-with-the-privacy-badger/60825
DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data
August 28, 2015DeconRNASeq…framework for #deconvolution of heterogeneous tissue samples http://bioinformatics.oxfordjournals.org/content/29/8/1083.long “App note” w/ very concise code snippet
30 lines of R?
lof paper in Nat Gen
August 28, 2015Analysis of #LOF variants & 20 risk factor phenotypes in 8.6K individuals identifies loci [both well known & new]
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3270.html
NATURE GENETICS | LETTER
Analysis of loss-of-function variants and 20 risk factor phenotypes in 8,554 individuals identifies loci influencing chronic disease
Alexander H Li,
Alanna C Morrison,
Christie Kovar,
L Adrienne Cupples,
Jennifer A Brody,
Linda M Polfus,
Bing Yu,
Ginger Metcalf,
Donna Muzny,
Narayanan Veeraraghavan,
Xiaoming Liu,
Thomas Lumley,
Thomas H Mosley,
Richard A Gibbs
& Eric Boerwinkle
Single-cell chromatin accessibility reveals principles of regulatory variation : Nature : Nature Publishing Group
August 28, 2015#SingleCell chromatin accessibility
http://www.nature.com/nature/journal/v523/n7561/full/nature14590.html >1.6k ATAC-seq expts; many on @ENCODE_NIH cell lines H1, GM12878 & K562
Multiple hypothesis testing in genomics – Goeman – 2014 – Statistics in Medicine – Wiley Online Library
August 17, 2015Multiple hypothesis testing in genomics
http://onlinelibrary.wiley.com/doi/10.1002/sim.6082/full Nice overview, comparing familywise error & FDR control + FDP estimation
http://www.few.vu.nl/~mavdwiel/HDDA/tutorial_multtest.pdf
QT:{{”
This paper presents an overview of the current state-of-the-art in multiple testing in genomics data from a user’s perspective. We describe methods for familywise error control, false discovery rate control and false discovery proportion estimation and confidence, both conceptually and practically, and explain when to use which type of error rate. We elaborate the assumptions underlying the methods, and discuss pitfalls in the interpretation of results. In our discussion we take into account the exploratory nature of genomics experiments, looking at selection of genes before or after testing, and at the role of validation experiments.
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seasonal effects on gene expression
August 9, 2015Widespread [25% genes] seasonal…expression reveals [circ]annual differences in…immunity, relevant for vaccination http://www.nature.com/ncomms/2015/150512/ncomms8000/full/ncomms8000.html
In addition to circadian rhythms, batch effects, now consider seasonal effects on gene expression
High-throughput DNA sequence data compression
August 9, 2015DNA sequence…#compression
http://bib.oxfordjournals.org/content/16/1/1.full Nice review comparing approaches on 2 axes: classic v Nextgen & reference-based v -free
Not much on LD-based approaches
Zexuan Zhu
Yongpeng Zhang
Zhen Ji
Shan He
Xiao Yang
Brief Bioinform (2015) 16 (1): 1-15.doi: 10.1093/bib/bbt087
First published online: December 3, 2013
Illumina poster of -seq experiments
August 9, 2015Poster of -Seq expts from @Illumina
http://www.illumina.com/content/dam/illumina-marketing/documents/applications/ngs-library-prep/ForAllYouSeqMethods.pdf Nextgen update to @Roche’s famous biochem. #pathway chart
http://biochemical-pathways.com/#/map/1
Originally Boehringer Mannheim chart of pathways
L1 – Somatic – Brain – Single cell DNA
August 7, 2015Cell Lineage Analysis in Human Brain Using Endogenous Retroelements http://www.sciencedirect.com/science/article/pii/S0896627314011374 Somatic events from #neuron #singlecell WGS
linkstream2 microblog 