Cyrface 2.0 – Bridging Cytoscape with R

Cyrface 2.0

:: DESCRIPTION

Cyrface establishes an interface between R and Cytoscape by using different Java-R libraries, e.g. Rserve, RCaller.

::DEVELOPER

Saez-Rodriguez Group

:: SCREENSHOTS

Cyrface

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package
  • Java
  • Cytoscape

:: DOWNLOAD

 Cyrface

:: MORE INFORMATION

Citation

F1000Res. 2013 Sep 19;2:192. doi: 10.12688/f1000research.2-192.v1. eCollection 2013.
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.
Gonçalves E, Saez-Rodriguez J.

phangorn 2.7.1 – Phylogenetic Analysis in R

phangorn 2.7.1

:: DESCRIPTION

phangorn is a package for phylogenetic reconstruction and analysis in the R language.

::DEVELOPER

Klaus Peter Schliep (klaus.kschliep@snv.jussieu.fr)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  phangorn

:: MORE INFORMATION

Citation

phangorn: phylogenetic analysis in R
Klaus Peter Schliep
Bioinformatics (2011) 27 (4): 592-593.

phytools 0.7-80 – Phylogenetic Tools in R

phytools 0.7-80

:: DESCRIPTION

phytools provides various functions for phylogenetic analysis, mostly relevant to comparative biology.

::DEVELOPER

REVELL LAB @ UMASS BOSTON

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Windows /Linux
  • R Package

:: DOWNLOAD

  phytools

:: MORE INFORMATION

Citation

Evolution. 2012 Sep;66(9):2697-707. doi: 10.1111/j.1558-5646.2012.01645.x. Epub 2012 Apr 29.
A new bayesian method for fitting evolutionary models to comparative data with intraspecific variation.
Revell LJ, Graham Reynolds R.

EBImage 4.35.0 – Image Processing and Analysis Toolkit for R

EBImage 4.35.0

:: DESCRIPTION

EBImage provides general purpose functionality for reading, writing, processing and analysis of images. Furthermore, in the context of microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors.

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 EBImage

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Apr 1;26(7):979-81. doi: 10.1093/bioinformatics/btq046.
EBImage–an R package for image processing with applications to cellular phenotypes.
Pau G, Fuchs F, Sklyar O, Boutros M, Huber W.

biomaRt 2.49.1 – Bridge from R to BioMart databases

biomaRt 2.49.1

:: DESCRIPTION

biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org).

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 biomaRt

:: MORE INFORMATION

Citation

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.
Durinck S, Spellman PT, Birney E, Huber W.
Nat Protoc. 2009;4(8):1184-91. doi: 10.1038/nprot.2009.97.

poRe 0.24 – An R package to enable Visualisation of Nanopore Sequencing data

poRe 0.24

:: DESCRIPTION

poRe (R_poRe) is a package for R that enables users to manipulate, organize, summarise and visualize MinION nanopore sequencing data.

::DEVELOPER

Mick Watson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 poRe

:: MORE INFORMATION

Citation

poRe: an R package for the visualization and analysis of nanopore sequencing data.
Watson M, Thomson M, Risse J, Talbot R, Santoyo-Lopez J, Gharbi K, Blaxter M.
Bioinformatics. 2014 Aug 29. pii: btu590.

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.

Rgb 1.6.1 – Genome Browser for R

Rgb 1.6.1

:: DESCRIPTION

Rgb (R genome browser) package is dedicated to memory efficient genome browsing strategies (both in scripts and interactive sessions) using the R scripting language. It includes classes and functions to manipulate genomic tracks, and a higher level interactive genome browser.

::DEVELOPER

Sylvain Mareschal

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 Rgb

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 21.
Rgb: a scriptable genome browser for R.
Mareschal S1, Dubois S, Lecroq T, Jardin F.

circlize 0.4.13 – Circular visualization in R

circlize 0.4.13

:: DESCRIPTION

circlize is an R package which implements circular visualization (http://circos.ca/) in R.

::DEVELOPER

Zuguang Gu <z.gu at dkfz.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R

:: DOWNLOAD

 circlize

:: MORE INFORMATION

Citation

circlize implements and enhances circular visualization in R.
Gu Z, Gu L, Eils R, Schlesner M, Brors B.
Bioinformatics. 2014 Jun 14. pii: btu393.

Seqinr 3.4-5 – Biological Sequences Retrieval and Analysis in R

Seqinr 3.4-5

:: DESCRIPTION

The seqinR package for the R environment is a library of utilities to retrieve and analyse biological sequences.

::DEVELOPER

Leonor Palmeira.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Seqinr

:: MORE INFORMATION

D. Charif, J. Thioulouse, J. R. Lobry and G. Perrière
Online synonymous codon usage analyses with the ade4 and seqinR packages
Bioinformatics (2005) 21 (4): 545-547