ResponseNet v.3 – Revealing Signaling and Regulatory Networks linking Genetic and Transcriptomic Screening data

ResponseNet v.3

:: DESCRIPTION

ResponseNet is a computational framework that identifies high-probability signaling and regulatory paths that connect input data sets.

::DEVELOPER

Yeger-Lotem Lab

:: SCREENSHOTS

ResponseNet

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W424-9. doi: 10.1093/nar/gkr359.
ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data.
Lan A, Smoly IY, Rapaport G, Lindquist S, Fraenkel E, Yeger-Lotem E.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W198-203. doi: 10.1093/nar/gkt532.
ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes–now with human data.
Basha O, Tirman S, Eluk A, Yeger-Lotem E.

AdaptML 1.0 – Partitioning of Gene Sequences according to their Genetic and Ecological Similarity

AdaptML 1.0

:: DESCRIPTION

AdaptML is a software package that will automatically partition groups of gene sequences according to both their genetic and ecological similarity.

::DEVELOPER

The Alm lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

 AdaptML

:: MORE INFORMATION

Citation

Science. 2008 May 23;320(5879):1081-5. doi: 10.1126/science.1157890.
Resource partitioning and sympatric differentiation among closely related bacterioplankton.
Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF.

isoscatR / scatR – Spatial Assignment using Genetic and Isotopic data

isoscatR / scatR

:: DESCRIPTION

scatR is an R package that implements smoothed and continuous assignment testing (SCAT) of genetic samples. These methods allow a researchers to infer smoothed allele frequencies across space using a Bayesian Gaussian process model fit to samples with known origin. Additionally, the package implements methods for the probabilistic estimatation of the spatial origin of samples using their genotypes.

::DEVELOPER

Novembre Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package

:: DOWNLOAD

 scatR

:: MORE INFORMATION

GESTE 2.0 – GEnetic STructure inference based on genetic and Environmental data

GESTE 2.0

:: DESCRIPTION

GESTE (GEnetic STructure inference based on genetic and Environmental data) is a Bayesian method to evaluate the effect that biotic and abiotic environmental factors (geographic distance, language, temperature, altitude, local population sizes, etc.) have on the genetic structure of populations. It can also be used to study spatial population processes, such as range expansions, by simply introducing longitude and latitude as the explanatory variables.

::DEVELOPER

Laboratoire d’Ecologie Alpine

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GESTE

:: MORE INFORMATION

Citation

Foll, M., and O.E. Gaggiotti, 2006.
Identifying the environmental factors that determine the genetic structure of Populations.
Genetics 174: 875-891.

GIPro 1.0 – Visualization of High-throughput Genetic and Physical Interaction data

GIPro 1.0

:: DESCRIPTION

GIPro is a Cytoscape plugin developed to allow integrative analysis and visualization of high-throughput genetic and physical interaction data in the context of protein complexes.

::DEVELOPER

The Wodak Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GIPro

:: MORE INFORMATION

popRange – A Spatially & Temporally Explicit Forward Population Genetic Simulator

popRange 1.1.3

:: DESCRIPTION

popRange is a forward genetic simulator, which incorporates large-scale genetic data with stochastic spatially and temporally explicit demographic and selective models.

::DEVELOPER

Kimberly McManus

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • R
  • Python

:: DOWNLOAD

 popRange

:: MORE INFORMATION

Citation

Source Code Biol Med. 2015 Apr 11;10:6. doi: 10.1186/s13029-015-0036-4. eCollection 2015.
popRange: a highly flexible spatially and temporally explicit Wright-Fisher simulator.
McManus KF

Kelviz v3.3.1 – Plot and Annotate Genetic data analysis results

Kelviz v3.3.1

:: DESCRIPTION

Kelviz is a graphing application designed to plot and annotate genetic data analysis results for easy review and publication. It is designed for use with Kelvin analysis results, but can make use of any data file that follows roughly the same conventions.

::DEVELOPER

Battelle Center for Mathematical Medicine

:: SCREENSHOTS

Kelviz

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

 Kelviz

:: MORE INFORMATION

Citation

Valentine-Cooper, J., et al. ”
Kelviz: A Graphing Tool For Statistical Evidence In Human Genetics.
Poster presented at: Road to Collaboration. NCH and OSU Human Genetics Community Symposium; 2014 May 20; Columbus, OH

BALL-SNP – Combining Genetic and Structural Information to Identify Candidate Non-synonymous SNPs

BALL-SNP

:: DESCRIPTION

BALL-SNPgp is the extension of the proof-of-concept tool BALL-SNP, a software tool based on the Biochemical Algorithms Library (BALL), a molecular modeling framework, providing robust and sophisticated algorithms on structural bioinformatics. BALL-SNPgp enables the assessment of multiple non-synonymous single nucleotide polymorphisms (nsSNPs) in a single protein by visualizing the mutated residues within the wild type structure, collecting available pathogenicity information from different databases, predicting binding pockets, protein stability changes and pathogenicity, as well as performing a cluster analysis on comprised amino acid substitutions

::DEVELOPER

Chair for clinical bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • BALL

:: DOWNLOAD

 BALL-SNPgp

:: MORE INFORMATION

Citation:

BALL-SNP: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms.
Mueller SC, Backes C, Kalinina OV, Meder B, Stöckel D, Lenhof HP, Meese E, Keller A.
Genome Med. 2015 Jul 1;7(1):65. doi: 10.1186/s13073-015-0190-y.