InterSIM 2.2.0 – Simulation of Inter-Related Genomic Datasets

InterSIM 2.2.0

:: DESCRIPTION

InterSIM is an R package for Simulation of Inter-Related Genomic Datasets. It generates three inter-related genomic datasets : methylation, gene expression and protein expression.

::DEVELOPER

Fridley Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

InterSIM

:: MORE INFORMATION

Citation:

Chalise P, Raghavan R, Fridley BL.
InterSIM: Simulation tool for multiple integrative ‘omic datasets’.
Comput Methods Programs Biomed. 2016 May;128:69-74. doi: 10.1016/j.cmpb.2016.02.011. Epub 2016 Feb 27. PMID: 27040832; PMCID: PMC4833453.

IntNMF 1.2.0 – Integrative Clustering of Multiple Genomic Dataset

IntNMF 1.2.0

:: DESCRIPTION

IntNMF is an R package for Integrative clustering of multiple genomic datasets with Non-negative matrix factorization (NMF).

::DEVELOPER

Fridley Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

IntNMF

:: MORE INFORMATION

Citation:

Chalise P, Fridley BL.
Integrative clustering of multi-level ‘omic data based on non-negative matrix factorization algorithm.
PLoS One. 2017 May 1;12(5):e0176278. doi: 10.1371/journal.pone.0176278. PMID: 28459819; PMCID: PMC5411077.

HiCPlotter 0.6.6 – Integrating HiC data with Genomic datasets

HiCPlotter 0.6.6

:: DESCRIPTION

HiCPlotter is a Python data visualization tool for integrating different data types with interaction matrixes.

::DEVELOPER

HiCPlotter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python
  • Numpy
  • Scipy
  • Cython
  • GNU Scientific Library

:: DOWNLOAD

 HiCPlotter

:: MORE INFORMATION

Citation

HiCPlotter integrates genomic data with interaction matrices.
Akdemir KC, Chin L.
Genome Biol. 2015 Sep 21;16(1):198.

MP3 1.0 – Prediction of Pathogenic Proteins in Metagenomic and Genomic Datasets

MP3 1.0

:: DESCRIPTION

MP3 is a standalone tool and web server for the prediction of pathogenic proteins in both genomic and metagenomic datasets.

::DEVELOPER

MetaBioSys laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MP3

:: MORE INFORMATION

Citation

MP3: a software tool for the prediction of pathogenic proteins in genomic and metagenomic data.
Gupta A, Kapil R, Dhakan DB, Sharma VK.
PLoS One. 2014 Apr 15;9(4):e93907. doi: 10.1371/journal.pone.0093907.