:: DESCRIPTION
BHC is an R/Bioconductor port of the fast novel algorithm for Bayesian agglomerative hierarchical clustering.
::DEVELOPER
Warwick Systems Biology Centre
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics 2009, 10:242
R/BHC: fast Bayesian hierarchical clustering for microarray data
Richard S Savage et al.
:: DESCRIPTION
HitSeekR is a web platform for analyzing high-throughput screening (HTS) data of various types, from miRNA (inhibitor) screens and RNAi assays to CRISPER/cas9 and drug response screens. It can accommodate, normalize, etc. small to ultra-large scale, and it turns your HTS data into a systems biology story.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Comprehensive analysis of high-throughput screens with HiTSeekR.
List M, Schmidt S, Christiansen H, Rehmsmeier M, Tan Q, Mollenhauer J, Baumbach J.
Nucleic Acids Res. 2016 Aug 19;44(14):6639-48. doi: 10.1093/nar/gkw554
:: DESCRIPTION
SPRINT (Simple Parallel R INTerface) is a parallel framework for R. It provides an easy access to high performance computing for the analysis of high throughput post genomic data using the statistical programming language R.
::DEVELOPER
SPRINT Team <sprint@ed.ac.uk>, EPCC, The University of Edinburgh,
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
SPRINT: a new parallel framework for R.
Hill J, Hambley M, Forster T, Mewissen M, Sloan TM, Scharinger F, Trew A, Ghazal P.
BMC Bioinformatics. 2008 Dec 29;9:558. doi: 10.1186/1471-2105-9-558.
:: DESCRIPTION
The package SyBiL is a Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks.
The R-package sybilSBML provides support for models written in SBML format.
The R-package sybilFCF computes extreme pathways and coupled reaction sets.
::DEVELOPER
Computational Cell Biology, Heinrich-Heine-Universität Düsseldorf
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Syst Biol. 2013 Nov 13;7:125. doi: 10.1186/1752-0509-7-125.
Sybil–efficient constraint-based modelling in R.
Gelius-Dietrich G, Desouki AA, Fritzemeier CJ, Lercher MJ.
:: DESCRIPTION
RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.
::DEVELOPER
Christoph Bartenhagen <christoph.bartenhagen at uni-muenster.de>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Jul 1;29(13):1679-81. doi: 10.1093/bioinformatics/btt198. Epub 2013 Apr 25.
RSVSim: an R/Bioconductor package for the simulation of structural variations.
Bartenhagen C, Dugas M.
:: DESCRIPTION
RReportGenerator provides a simple and user-friendly graphical user interface (GUI) allowing to run routine statistical analysis using R via predefined analysis scenarios in a local and independent manner. Of course, the large variety of additional libraries on CRAN and Bioconductor may be used with the analysis scenarios. The results (text, figures and tables) are automatically assembled into a report in pdf- (or dvi) format. This may be accompanied by an additional file(s) for exporting (specific) results to other applications (spread-sheet programs, web-browser etc).
::DEVELOPER
Wolfgang Raffelsberger at LBGI : Laboratoire de bioinformatique et de génomique intégratives
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2008 Jan 15;24(2):276-8. Epub 2007 Nov 24.
RReportGenerator: automatic reports from routine statistical analysis using R.
Raffelsberger W, Krause Y, Moulinier L, Kieffer D, Morand AL, Brino L, Poch O.
:: DESCRIPTION
The Funmap package is developed to identify quantitative trait loci (QTL) for a longitudinal, or vectorized, phenotypic trait as based on the Funmap model
::DEVELOPER
Center for Statistical Genetics, Penn State University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ma, C. X., G. Casella, and R. L. Wu, 2003.
Functional mapping of quantitative trait loci underlying the character process: A theoretical framework.
Genetics 161(4): 1751-1762.
:: DESCRIPTION
The R/fGWAS2 (Functional Genome-wide Association Studies) is developed as a new package for genome-wide association studies based on a single SNP analysis . It provides three separate methods.
::DEVELOPER
Center for Statistical Genetics, Penn State University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jiahan Li, Kiranmoy Das, Guifang fu, Runze Li and Rongling Wu.
The Bayesian Lasso for Genome-wide Associations Studies.
Bioinformatics (2011) 27 (4): 516-523. doi:
:: DESCRIPTION
CARMAweb (Comprehensive R-based Microarray Analysis web service) is a web application designed for the analysis of microarray data. CARMAweb performs data preprocessing (background correction, quality control and normalization), detection of differentially expressed genes, cluster analysis, dimension reduction and visualization, classification, and Gene Ontology-term analysis. This web application accepts raw data from a variety of imaging software tools for the most widely used microarray platforms: Affymetrix GeneChips, spotted two-color microarrays and Applied Biosystems (ABI) microarrays.
::DEVELOPER
Genomics & Bioinformatics Graz, Graz University of Technology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rainer J., Sanchez-Cabo F., Stocker G., Sturn A. and Trajanoski Z.
CARMAweb: comprehensive R- and Bioconductor-based web service for microarray data analysis
Nucleic Acids Research, 2006 vol 34(Web Server Issue):W498-503.
:: DESCRIPTION
ClashScore generate a percentile plot of ClashScore versus Resolution like that found in the X-Ray Verification Task Force’s recommendation to wwPDB.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
ClashScore is free software available under the terms of its own BSD-style license.
