Tag: R package

phylolm 2.6.2 – R package for Fitting Phylogenetic Linear Regression models

phylolm 2.6.2

:: DESCRIPTION

phylolm is an R package providing a function for fitting phylogenetic linear regression models. The likelihood is calculated with an algorithm that is linear in the number of tips in the tree. The package also provides a function for simulating continuous traits along the tree.

::DEVELOPER

Lam Si Tung Ho

:: REQUIREMENTS

  • Linux/windows/ MacOsX
  • R Package

:: DOWNLOAD

 phylolm

:: MORE INFORMATION

Citation

Syst Biol. 2014 Feb 4. [Epub ahead of print]
A linear-time algorithm for Gaussian and non-Gaussian trait evolution models.
Ho LS, Ané C.

Haplosuite 1.1 – R package for Haplotype Clustering and Visualization

Haplosuite 1.1

:: DESCRIPTION

Haplosuite is a collection of R codes, including HAPLOSIM and HAPVISUAL, for the purpose of clustering haplotypes and haplotype visualization

::DEVELOPER

Saw Swee Hock School of Public Health

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package

:: DOWNLOAD

 Haplosuite

:: MORE INFORMATION

Citation

Teo YY and Small KS. (2010)
A novel method for haplotype clustering and visualization.
Genetic Epidemiology, 34(1), 34-41

PEA-m5C 0.1.3 – An R package for Plant m5C analysis

PEA-m5C 0.1.3

:: DESCRIPTION

PEA-m5C is an accurate transcriptome-wide m5C modification predictor under machine learning framework

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

PEA-m5C

:: MORE INFORMATION

Citation

Song J, Zhai J, Bian E, Song Y, Yu J, Ma C.
Transcriptome-Wide Annotation of m5C RNA Modifications Using Machine Learning.
Front Plant Sci. 2018 Apr 18;9:519. doi: 10.3389/fpls.2018.00519. Erratum in: Front Plant Sci. 2018 Nov 30;9:1762. PMID: 29720995; PMCID: PMC5915569.

WOMBSOFT – R package for Wombling Analyses

WOMBSOFT

:: DESCRIPTION

WOMBSOFT is a collection of R functions Wombling-based that analyse individually geo-referenced multilocus genotypes for the inferences of genetic boundaries between populations. The software produces two maps.

::DEVELOPER

Laboratoire d’Ecologie Alpine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  WOMBSOFT

:: MORE INFORMATION

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.

BayesMendel 2.1-7 – R package for Mendelian Risk Prediction

BayesMendel 2.1-7

:: 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.

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.

maSigPro 1.62.0 – R package for the analysis of Microarray and RNA-seq Time Series data

maSigPro 1.62.0

:: 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.

RCircos 1.2.1 – R package for Circos 2D track plots

RCircos 1.2.1

:: 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.

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

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