CNet – Discovery of Clinically Associated, Combinatory Genomic Signatures

CNet

:: DESCRIPTION

CNet is a JAVA package that detects groups of genomic signatures that are associated with clinical and phenotypical outcomes.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux / Windows
Java

:: DOWNLOAD

CNet

:: MORE INFORMATION

Citation:

Jia P, Pei G, Zhao Z.
CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures.
Bioinformatics. 2019 Dec 15;35(24):5207-5215. doi: 10.1093/bioinformatics/btz441. PMID: 31141125; PMCID: PMC6954662.

ASSIGN 1.6.0 – Adaptive Profiling of Genomic Signatures

ASSIGN 1.6.0

:: DESCRIPTION

ASSIGN (Adaptive Signature Selection and InteGratioN) is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples.

::DEVELOPER

Johnson lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows/ MacOsX
R
BioConductor

:: DOWNLOAD

ASSIGN

:: MORE INFORMATION

Citation

ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways.
Shen Y, Rahman M, Piccolo SR, Gusenleitner D, El-Chaar NN, Cheng L, Monti S, Bild AH, Johnson WE.
Bioinformatics. 2015 Jun 1;31(11):1745-53. doi: 10.1093/bioinformatics/btv031.

Genome Classifier – Genomic Signature Classifier

Genome Classifier

:: DESCRIPTION

Genome Classifier (genomeclass) is a python/pyrex implementation of the Bayesian classifier of genomic signatures.

::DEVELOPER

Sandberg Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX
Python

:: DOWNLOAD

Genome Classifier

:: MORE INFORMATION

Citation

Genome Res. 2001 Aug;11(8):1404-9.
Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier.
Sandberg R, Winberg G, Bränden CI, Kaske A, Ernberg I, Cöster J.