BHC 1.1.0 – Bayesian Hierarchical Clustering for R

BHC 1.1.0

:: 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

  • Windows/Linux/ MacOsX
  • R package

:: DOWNLOAD

 BHC

:: MORE INFORMATION

Citation

BMC Bioinformatics 2009, 10:242
R/BHC: fast Bayesian hierarchical clustering for microarray data
Richard S Savage et al.

HitSeekR – High-Throughput Screening Kit for R

HitSeekR

:: 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

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

HitSeekR

:: 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

 

SPRINT 1.0.7 – Parallel Framework for R

SPRINT 1.0.7

:: 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

  • Linux/ MacOsX
  • R package

:: DOWNLOAD

 SPRINT

:: 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.

SyBiL 2.1.5 / sybilSBML 3.0.5 / sybilFCF 0.2.1 – Systems Biology Library for R

SyBiL 2.1.5 / sybilSBML 3.0.5 / sybilFCF 0.2.1

:: 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

 SyBiL / sybilSBML  / sybilFCF

:: 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.

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.

Rgb 1.4.1 – Genome Browser for R

Rgb 1.4.1

:: 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 0.3.6 – Circular visualization in R

circlize 0.3.6

:: 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.

Basic4Cseq 1.6.0 – an R/Bioconductor package for analyzing 4C-seq data

Basic4Cseq 1.6.0

:: 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.

poRe 0.17 – An R package to enable Visualisation of Nanopore Sequencing data

poRe 0.17

:: 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.

biomaRt 2.27.2 – Bridge from R to BioMart databases

biomaRt 2.27.2

:: 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.