TimesVector 1.5 – Analysis of Time Series Transcriptome data from multiple Phenotypes

TimesVector 1.5

:: DESCRIPTION

TimesVector is a triclustering tool for clustering time-series data that comprises multiple conditions, or phenotypes.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R

:: DOWNLOAD

TimesVector

:: MORE INFORMATION

Citation

Jung I, Jo K, Kang H, Ahn H, Yu Y, Kim S.
TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes.
Bioinformatics. 2017 Dec 1;33(23):3827-3835. doi: 10.1093/bioinformatics/btw780. PMID: 28096084.

DeepGS 1.2 – Predicting Phenotypes from Genotypes using Deep Learning

DeepGS 1.2

:: DESCRIPTION

DeepGS is a R package for predicting phenotypes from genotypes using deep learning techniques.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

DeepGS

:: MORE INFORMATION

Citation

Ma W, Qiu Z, Song J, Li J, Cheng Q, Zhai J, Ma C.
A deep convolutional neural network approach for predicting phenotypes from genotypes.
Planta. 2018 Nov;248(5):1307-1318. doi: 10.1007/s00425-018-2976-9. Epub 2018 Aug 12. PMID: 30101399.

opm 1.1.0 – Analysing Phenotype Microarray and Growth Curve Data

opm 1.1.0

:: DESCRIPTION

opm is an R package designed to analyse multidimensional OmniLog phenotype microarray (PM) data.

::DEVELOPER

Leibniz Institute DSMZ

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 opm

 :: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 15;29(14):1823-4. doi: 10.1093/bioinformatics/btt291. Epub 2013 Jun 5.
opm: an R package for analysing OmniLog(R) phenotype microarray data.
Vaas LA1, Sikorski J, Hofner B, Fiebig A, Buddruhs N, Klenk HP, Goker M.

PhenoMan 1.0RC – Exploration and Management of Phenotype data

PhenoMan 1.0RC

:: DESCRIPTION

Phenoman is freeware that provides approaches for efficient exploration and management of phenotype data.

::DEVELOPER

PhenoMan team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python
  • R package

:: DOWNLOAD

 PhenoMan

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Feb 1;30(3):442-4. doi: 10.1093/bioinformatics/btt682. Epub 2013 Dec 12.
PhenoMan: phenotypic data exploration, selection, management and quality control for association studies of rare and common variants.
Li B1, Wang G, Leal SM.

Coevol 1.5 – Correlated Evolution of Substitution Rates and Phenotypes

Coevol 1.5

:: DESCRIPTION

Coevol is a Bayesian MCMC software for comparative analyses combining molecular data and continuous characters (e.g. ecological variables or life-history traits.)

::DEVELOPER

Nicolas Lartillot (nicolas.lartillot@umontreal.ca)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

 Coevol

:: MORE INFORMATION

Citation

Lartillot N, Poujol R.
A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters.
Mol Biol Evol. 2011 Jan;28(1):729-44. Epub 2010 Oct 6.

MamPhEA – Mammalian Phenotype Enrichment Analysis

MamPhEA

:: DESCRIPTION

MamPhEA is a web application dedicated to understanding functional properties of mammalian gene sets based on mouse-mutant phenotypes.

::DEVELOPER

MamPhEA team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 1;26(17):2212-3. doi: 10.1093/bioinformatics/btq359. Epub 2010 Jul 6.
MamPhEA: a web tool for mammalian phenotype enrichment analysis.
Weng MP1, Liao BY.

PINES – Phenotype-Informed Noncoding Element Scoring

PINES

:: DESCRIPTION

PINES evaluates the functional impact of noncoding variants by integrating diverse epigenetic annotations, utilizing genomic annotations most relevant to phenotypes of interest.

::DEVELOPER

SUNYAEV LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • R

:: DOWNLOAD

PINES

:: MORE INFORMATION

Citation

Bodea CA, Mitchell AA, Bloemendal A, Day-Williams AG, Runz H, Sunyaev SR.
PINES: phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants.
Genome Biol. 2018 Oct 25;19(1):173. doi: 10.1186/s13059-018-1546-6. PMID: 30359302; PMCID: PMC6203199.

SIMLAPLOT 1.0 – Visualize Genotype and Phenotype Relationship

SIMLAPLOT 1.0

:: DESCRIPTION

SIMLAPLOT is a software for visualizing different ways in which continuous covariates may influence the genotype-specific risk for complex human diseases. The purpose of our study was to examine continuous covariates in the Genetic Analysis Workshop 15 simulated data set using our novel graphical display tool, with knowledge of the answers. The generated plots provide information about genetic models for the simulated continuous covariates and may help identify the single-nucleotide polymorphisms associated with the underlying quantitative trait loci.

::DEVELOPER

Duke Molecular Physiology Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SIMLAPLOT

:: MORE INFORMATION

Citation

Xuejun Qin,et al
Visualizing genotype × phenotype relationships in the GAW15 simulated data
BMC Proc. 2007; 1(Suppl 1): S132.

GENOSIM v4 – Simulate Genotypes, Breeding Values, and Phenotypes

GENOSIM v4

:: DESCRIPTION

GENOSIM is a set of programs to simulate genotypes, breeding values, phenotypes, and DNA sequence read depth and to resolve SNP conflicts between parent and offspring genotypes

::DEVELOPER

Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Fortron

:: DOWNLOAD

  GENOSIM

:: MORE INFORMATION

dbVOR 1.12 – Phenotype and Genotype Database System

dbVOR 1.12

:: DESCRIPTION

dbVOR is a database system for importing pedigree, phenotype and genotype data and exporting selected subsets.

::DEVELOPER

Division of Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • MySQL
  • MySQLDB

:: DOWNLOAD

 dbVOR

:: MORE INFORMATION

Citation

dbVOR: a database system for importing pedigree, phenotype and genotype data and exporting selected subsets
Baron RV, Conley YP, Gorin MB, Weeks DE.
BMC Bioinformatics. 2015 Mar 18;16(1):91.

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