Bedshift v1.1.1 – Bedfile Perturbation tool

Bedshift v1.1.1

:: DESCRIPTION

Bedshift is a tool for randomly perturbing BED file regions. The perturbations supported on regions are shift, drop, add, cut, and merge. This tool is particularly useful for creating test datasets for various tasks, since there often is no ground truth dataset to compare to. By perturbing a file, a pipeline or analysis can be run on both the perturbed file and the original file, then be compared.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

Bedshift

:: MORE INFORMATION

Citation

Gu A, Cho HJ, Sheffield NC.
Bedshift: perturbation of genomic interval sets.
Genome Biol. 2021 Aug 20;22(1):238. doi: 10.1186/s13059-021-02440-w. PMID: 34416909; PMCID: PMC8379854.

NEXCADE 2.1 – Perturbation Analysis for Complex Networks

NEXCADE 2.1

:: DESCRIPTION

Nexcade (Network EXtinction casCADEs) is an automated and interactive program for analysing complex systems that can be conceptualized by networks, and represented as interconnected matrices of interactions. The analytical framework employs a graph theoretical approach for inducing various kinds of perturbations on networks such as extinction cascade simulations, focusing on the changes in topology and connectivity of the network as a function of the perturbation. Perturbations are induced in a user-defined manner followed by analysis of the resulting sub-networks.

::DEVELOPER

Suresh Babu & Dr. Gitanjali Yadav

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

NEXCADE

:: MORE INFORMATION

Citation

PLoS One. 2012;7(8):e41827. doi: 10.1371/journal.pone.0041827. Epub 2012 Aug 3.
NEXCADE: perturbation analysis for complex networks.
Yadav G1, Babu S.

PeTTSy 1.0 – Perturbation Theory Toolbox for Systems

PeTTSy 1.0

:: DESCRIPTION

PeTTSy is a GUI based Matlab toolbox which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation based models.

::DEVELOPER

Warwick Systems Biology Centre

:: SCREENSHOTS

:: REQUIREMENTS

Linux /Windows/ MacOsX
MatLab

:: DOWNLOAD

PeTTSy

:: MORE INFORMATION

Citation

PeTTSy: a computational tool for perturbation analysis of complex systems biology models.
Domijan M, Brown PE, Shulgin BV, Rand DA.
BMC Bioinformatics. 2016 Mar 10;17(1):124. doi: 10.1186/s12859-016-0972-2.