Search Results for "script-api.jar"

...For theoretical background please refer to 'MANTIS: an R package that simulates multilocus models of pathogen evolution' (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0598-9 OPEN ACCESS) At the moment, MANTIS is not available on CRAN. To build a source package of MANTIS, use the script buildPackage.R To install MANTIS use 'install.packages(file.tar.gz,type="src",repo=NULL)' To test use test_V3.3_code.R Contact the main author of the publication above for further details. Have fun!

The NOFI ranking algorithm has been developed to assign low priority to fragment ions affected by interference. The implementation is an R script that can be customized. A future version will contain a modular version. The outline is as follows: 1) The input contains the list of SWATH fragment ion XICs from the identified and quantified peptides by software tools such as Skyline and OpenSWATH. 2) The first step in NOFI is the computation of the 4 attributes (RTd, FWHMd, IRd and IRrep) used to represent each fragment ion as a vector. 3) Multivariate outlier detection techniques are used to rank all the fragment ions from each peptide. 4) Several figures are generated (a pdf file) to visualize the effect of the Top-N fragment ions over different indicators. 5) The user can choose the number of top fragment ions per peptide, thereby utilizing the optimal subset of high priority Top-N NOFIs for quantification while excluding the impaired fragment ions.

RMol is an R script with a collection of functions to link information of SD/Molfile structure databases with powerful graph analysis packages in R.

An R script written by Martin Turjak, implementing a newly developed method for evaluating synapomorphy on phylogenetic trees. For details see: http://sourceforge.net/p/synapomorphy

QiSampler is an R script used as a command-line bioinformatics tool that evaluates the prioritization done by scoring schemes and experimental parameters of high throughput biological datasets.