SPECifIC – Sub-Pathway Extractor and Enricher

SPECifIC

:: DESCRIPTION

SPECifIC is a network-based systems biology tool capable of extracting disease-perturbed subpathways within pathway networks in connection with expression data.

::DEVELOPER

SPECifIC team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / web server

:: DOWNLOAD

SPECifIC

:: MORE INFORMATION

Citation:

Detecting Disease Specific Pathway Substructures through an Integrated Systems Biology Approach.
Alaimo S, Marceca GP, Ferro A, Pulvirenti A.
Noncoding RNA. 2017 Apr 19;3(2). pii: E20. doi: 10.3390/ncrna3020020.

BioAtlas – Location-specific analysis of Microbial profiles

BioAtlas

:: DESCRIPTION

BioAtlas is a web service, primarily designed for biologists to explore where 16S rRNA strains classified from bacteria and/or archaea taxonomy are found, whether it be geographical and/or host-oriented locations.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Interactive microbial distribution analysis using BioAtlas.
Lund JB, List M, Baumbach J.
Nucleic Acids Res. 2017 Jul 3;45(W1):W509-W513. doi: 10.1093/nar/gkx304.

SVEngine – Allele Specific and Haplotype Aware Structural Variants Simulator

SVEngine

:: DESCRIPTION

SVEngine (Structural Variants Engine) is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Python

:: DOWNLOAD

SVEngine

:: MORE INFORMATION

Citation

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy081.
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.
Xia LC, Ai D, Lee H, Andor N, Li C, Zhang NR, Ji HP