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Jump to Shiny Apps, R Packages, Other


The following make use of the Shiny R package to create interactive web applications.

A tool to interact with the CamCaP and other prostate data sets as presented in the paper Dunning MJ, Vowler SL, Lalonde E, Ross-Adams H, Boutros P, Mills IG, Lynch AG, Lamb AD (2017) Mining Human Prostate Cancer Datasets: The “camcAPP” Shiny App. EBioMedicine http://dx.doi.org/10.1016/j.ebiom.2017.02.022

A tool to implement an improved estimate of glomerular filtration, as presented in the paper Janowitz T, Williams EH, Marshall A, Ainsworth N, Thomas PB, Sammut SJ, Shepherd S, White J, Mark PB, Lynch AG, Jodrell DI, Tavaré S, and Earl H (2017) 
New Model for Estimating Glomerular Filtration Rate in Patients With CancerJournal of Clinical Oncology

A simple tool to allow interactive investigation of cellularity and ploidy calls. Especially in the case where different tools provide different estimates. A revision of the tool presented in Lynch AG (2015) "Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimatesF1000Research 4:1407 (doi: 10.12688/f1000research.7453.1) 

(Apologies for the name, but it came from a segmentation pipeline called Crambled-seg)


The following packages are all written for the R environment for statistical computing


(Lynch AG and Dunning MJ)

A package to aid the detection of sample mis-mappings when dealing with expression and genotype data. 

See the paper Lynch AG, Dunning MJ, Chin S-F, Caldas C, Tavaré S and Curtis C (2012)  "Calling Sample Mix-ups in Cancer Population Studies" PLoS ONE 7(8):e41815


Spyrou C, Cairns J, Stark R, Lynch AG and Tavaré S

An implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.


Dunning MJ, Smith ML, Cairns J, Lynch AG and Ritchie ME

A package to facilitate the analysis of Illumina BeadArray data from its rawest format. When dealing with the probe-level (rather than summarized) data that Illumina scanners can produce, new quality control and analysis approaches become possible, and some are provided.

Smith ML and Lynch AG

Provides a novel compression schema for the representation of BeadArray data, and tools for converting to and from this format


Lynch AG

Defining a suite of colours that my colleagues might find useful. 

Andy Lynch,
2 Jul 2012, 10:14