Tag: Bioconductor

Piano 2.8.0 – An R/Bioconductor package for Gene Set Analysis

Piano 2.8.0

:: DESCRIPTION

Piano is an R/Bioconductor package that is used for running gene set analysis and is also capable of performing basic microarray analysis.

:: DEVELOPER

Systems & Synthetic Biology – SYSBIO, Chalmers University of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 Piano

:: MORE INFORMATION

Citation

Väremo, L., Nielsen, J. and Nookaew, I. (2013)
Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods.
Nucleic Acids Research. 41 (8), 4378-4391. DOI:10.1093/nar/gkt111

KEGGgraph 1.52.0 – A Graph Approach to KEGG PATHWAY in R and Bioconductor

KEGGgraph 1.52.0

:: DESCRIPTION

KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.

::DEVELOPER

Jitao David Zhang <jitao_david.zhang at roche.com>, Stefan Wiemann 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 KEGGgraph

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jun 1;25(11):1470-1. doi: 10.1093/bioinformatics/btp167. Epub 2009 Mar 23.
KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor.
Zhang JD, Wiemann S.

Bioconductor 3.13 – Open Source Software for Bioinformatics

Bioconductor 3.13

:: DESCRIPTION

Bioconductor is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. It is based primarily on the R programming language.

::DEVELOPER

Bioconductor Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Bioconductor

:: MORE INFORMATION

Publications

Basic4Cseq 1.28.0 – an R/Bioconductor package for analyzing 4C-seq data

Basic4Cseq 1.28.0

:: DESCRIPTION

Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included.

::DEVELOPER

Carolin Walter <carolin.walter at uni-muenster.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/ MacOsX
  • R
  • BioCOnductor

:: DOWNLOAD

 Basic4Cseq

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 30. pii: btu497. [Epub ahead of print]
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data.
Walter C, Schuetzmann D, Rosenbauer F, Dugas M.

RSVSim 1.24.0 – an R/Bioconductor package for the Simulation of Structural Variations

RSVSim 1.24.0

:: 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

  • Linux/Windows/ MacOsX
  • R
  • BioCOnductor

:: DOWNLOAD

 RSVSim

:: 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.

R-Cloud Workbench 1.2.0 – Remote Access to R/Bioconductor on EBI’s 64-bit Linux Cluster

R-Cloud Workbench 1.2.0

:: DESCRIPTION

R-Cloud Workbench is a software to remote access to R/Bioconductor on EBI’s 64-bit Linux Cluster. Start the workbench by downloading the package for your operating system (Macintosh or Windows), or via Java Web Start, and you will get access to an instance of R running on one of EBI’s powerful machines. You can install additional packages, upload your own data, work with graphics and collaborate with colleagues, all as if you are running R locally, but unlimited by your machine’s memory, processor or data storage capacity.

::DEVELOPER

EBI.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 R-Cloud

:: MORE INFORMATION

 

Citation:

Bioinformatics. 2011 Mar 15;27(6):867-9. Epub 2011 Jan 13.
A pipeline for RNA-seq data processing and quality assessment.
Goncalves A, Tikhonov A, Brazma A, Kapushesky M.

 

CARMAweb 1.3 – R- and Bioconductor-based web service for Microarray Data Analysis

CARMAweb 1.3

:: 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

 CARMAweb

:: 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.