NVT 1.0 – R package for the Assessment of RNA-Seq Normalization methods

NVT 1.0

:: DESCRIPTION

NVT (NORMALIZATION VISUALIZATION TOOL) is an R package for the assessment of RNA-Seq normalization methods.

::DEVELOPER

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

NVT

:: MORE INFORMATION

Citation:

Bioinformatics, 32 (23), 3682-3684 2016 Dec 1
NVT: A Fast and Simple Tool for the Assessment of RNA-seq Normalization Strategies
Thomas Eder, Florian Grebien, Thomas Rattei

Phybase 2.0 – R package for Phylogenetic Analysis

Phybase 2.0

:: DESCRIPTION

PHYBASE provides functions to read, write, manipulate, simulate, estimate, and summarize phylogenetic trees (gene trees and species trees).

::DEVELOPER

Phylogenetics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/ Windows / Linux
  • R

:: DOWNLOAD

Phybase

:: MORE INFORMATION

Citation

Bioinformatics, 26 (7), 962-3 2010 Apr 1
Phybase: An R Package for Species Tree Analysis
Liang Liu 1, Lili Yu

VRMLGen 1.4.6 – An R Package for 3D Data Visualization on the Web

VRMLGen 1.4.6

:: DESCRIPTION

VRMLGen is a free R software package to generate 3D representations of biological data in the Virtual Reality Markup Language

::DEVELOPER

VRMLGen team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

VRMLGen

:: MORE INFORMATION

Citation

Enrico Glaab, Jonathan M. Garibaldi, Natalio Krasnogor
vrmlgen: An R Package for 3D Data Visualization on the Web
Journal of Statistical Software, 2010 DOI: 10.18637/jss.v036.i08

APCluster 1.4.8 – Affinity Propagation Clustering

APCluster 1.4.8

:: DESCRIPTION

The apcluster package implements Frey’s and Dueck’s Affinity Propagation clustering in R. The algorithms are largely analogous to the Matlab code published by Frey and Dueck. The package further provides an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 APCluster for R

:: MORE INFORMATION

Citation

U. Bodenhofer, A. Kothmeier, and S. Hochreiter (2011).
APCluster: an R package for affinity propagation clustering.
Bioinformatics 27:2463-2464

KeBABS 1.20.0 – R Package for Kernel-Based Analysis of Biological Sequences

KeBABS 1.20.0

:: DESCRIPTION

The KeBABS package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define similarity measures between sequences.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

  KeBABS

:: MORE INFORMATION

Citation

KeBABS: an R package for kernel-based analysis of biological sequences.
Palme J, Hochreiter S, Bodenhofer U.
Bioinformatics. 2015 Mar 25. pii: btv176.

maSigPro 1.58.0 – R package for the analysis of Microarray and RNA-seq Time Series data

maSigPro 1.58.0

:: DESCRIPTION

maSigPro (MicroArray Significant Profiles)is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R Package
  • BioConductor

:: DOWNLOAD

 maSigPro

:: MORE INFORMATION

Citation

Next maSigPro: updating maSigPro Bioconductor package for RNA-seq time series.
Nueda MJ, Tarazona S, Conesa A.
Bioinformatics. 2014 Jun 3. pii: btu333.

Bioinformatics. 2006 May 1;22(9):1096-102. Epub 2006 Feb 15.
maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments.
Conesa A1, Nueda MJ, Ferrer A, Talón M.

methylKit 0.99.2 – R package for DNA methylation analysis

methylKit 0.99.2

:: DESCRIPTION

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. It can potentially handle whole-genome bisulfite sequencing data if proper input format is provided.

::DEVELOPER

BIMSB bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 methylKit

:: MORE INFORMATION

Citaton

Genome Biol. 2012 Oct 3;13(10):R87. [Epub ahead of print]
methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE.

RCircos 1.1.3 – R package for Circos 2D track plots

RCircos 1.1.3

:: DESCRIPTION

RCircos package provides a simple and flexible way to generate Circos 2D track plot images for genomic data visualization. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label.

::DEVELOPER

Hongen Zhang <hzhang at mail.nih.gov>, Sean Davis @NCI

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package

:: DOWNLOAD

  RCircos

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Aug 10;14:244. doi: 10.1186/1471-2105-14-244.
RCircos: an R package for Circos 2D track plots.
Zhang H, Meltzer P, Davis S.

BayesMendel 2.1-1 – R package for Mendelian Risk Prediction

BayesMendel 2.1-1

:: DESCRIPTION

BayesMendel is an R package for Mendelian risk prediction. It includes R implementation of the BRCAPRO and CRCAPRO models, as well as functionality to adapt BRCAPRO and CRCAPRO to specific population and to develop new Mendelian risk prediction models for other syndromes.

::DEVELOPER

BayesMendel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R package

:: DOWNLOAD

 BayesMendel

:: MORE INFORMATION

Citation

BayesMendel: an R environment for Mendelian risk prediction.
Chen S, Wang W, Broman KW, Katki HA, Parmigiani G.
Stat Appl Genet Mol Biol. 2004;3:Article21. Epub 2004 Sep 17.

genomation 0.99.7 – R package for Graphics and Operations for Genomic

genomation 0.99.7

:: DESCRIPTION

Genomation is an R package for genomic feature analysis and annotation by extending bioconductor packages.

::DEVELOPER

BIMSB bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 genomation

:: MORE INFORMATION

Citation

genomation: a toolkit to summarize, annotate and visualize genomic intervals.
Akalin A, Franke V, Vlahoviček K, Mason CE, Schübeler D.
Bioinformatics. 2014 Nov 21. pii: btu775.