MotifNet – Web-server for Network Motif analysis

MotifNet

:: DESCRIPTION

MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes.

::DEVELOPER

Yeger-Lotem Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Smoly IY, Lerman E, Ziv-Ukelson M, Yeger-Lotem E.
MotifNet: a web-server for network motif analysis.
Bioinformatics. 2017 Jun 15;33(12):1907-1909. doi: 10.1093/bioinformatics/btx056. PMID: 28165111.

mfinder 1.21 – Network Motifs Detection tool

mfinder 1.21

:: DESCRIPTION

mfinder is a software tool for network motifs detection.

::DEVELOPER

Uri Alon Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 mfinder

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Jul 22;20(11):1746-58. Epub 2004 Mar 4.
Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs.
Kashtan N, Itzkovitz S, Milo R, Alon U.

JANet – Javascript AgeFactDB Network-viewer

JANet

:: DESCRIPTION

JANet is a specialized 3D Network Exploration and Visualization for Lifespan Data Exploration from AgeFactDB.

::DEVELOPER

Medical Systems Biology, University of Ulm

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

JANet

:: MORE INFORMATION

Citation

Hühne R, Kessler V, Fürstberger A, Kühlwein S, Platzer M, Sühnel J, Lausser L, Kestler HA.
3D Network exploration and visualisation for lifespan data.
BMC Bioinformatics. 2018 Oct 23;19(1):390. doi: 10.1186/s12859-018-2393-x. PMID: 30352578; PMCID: PMC6199797.

SpectralNET 1.0 – Analyze Networks of Interactions

SpectralNET 1.0

:: DESCRIPTION

SpectralNET is a tool to analyze networks of interactions, such as chemical-genetic networks

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  SpectralNET

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2005 Oct 19;6:260.
SpectralNET–an application for spectral graph analysis and visualization.
Forman JJ, Clemons PA, Schreiber SL, Haggarty SJ.

AccNET V1.2 – Accessory Genome Constellation Network

AccNET V1.2

:: DESCRIPTION

AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms.

:: DEVELOPER

irycis Bioinfo

:: REQUIREMENTS

  • Linux / Window
  • Perl

:: DOWNLOAD

AccNET

:: MORE INFORMATION

Citation

Lanza VF, Baquero F, de la Cruz F, Coque TM.
AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks.
Bioinformatics. 2017 Jan 15;33(2):283-285. doi: 10.1093/bioinformatics/btw601. Epub 2016 Sep 23. PMID: 27663497.

PLACNET 1.04 / PLACNETw – Plasmid Constellation Network project

PLACNET 1.04 / PLACNETw

:: DESCRIPTION

PLACNET is a graph-based tool for reconstruction of plasmids from next generation sequence pair-end datasets.

PLACNETw, a web tool based on PLACNET, provides an interactive graphic interface, automates BLAST searches, and extracts the relevant information for decision making.

:: DEVELOPER

irycis Bioinfo

:: REQUIREMENTS

  • Linux / Window
  • Python

:: DOWNLOAD

PLACNET / PLACNETw

:: MORE INFORMATION

Citation

Lanza VF, de Toro M, Garcillán-Barcia MP, Mora A, Blanco J, Coque TM, de la Cruz F.
Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences.
PLoS Genet. 2014 Dec 18;10(12):e1004766. doi: 10.1371/journal.pgen.1004766. PMID: 25522143; PMCID: PMC4270462.

Vielva L, de Toro M, Lanza VF, de la Cruz F.
PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes.
Bioinformatics. 2017 Dec 1;33(23):3796-3798. doi: 10.1093/bioinformatics/btx462. PMID: 29036591.

PhyloSketch 0.1.8 – Sketch rooted Phylogenetic Trees and networks

PhyloSketch 0.1.8

:: DESCRIPTION

PhyloSketch is an interactive program for sketching rooted phylogenetic trees and networks. The program reports on some of mathematical properties of the network. The program can import and export rooted phylogenetic trees or networks in (extended) Newick format.

::DEVELOPER

the Algorithms in Bioinformatics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

PhyloSketch

:: MORE INFORMATION

NetSig – Network-based Discovery from Cancer Genomes

NetSig

:: DESCRIPTION

NetSig is a robust statistic software that integrates protein interaction networks with data from 4,742 tumor exomes. NetSig can accurately classify known driver genes in 60% of tested tumor types and predicts 62 new driver candidates.

::DEVELOPER

Lage Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NetSig

:: MORE INFORMATION

Citation

Horn H, Lawrence MS, Chouinard CR, Shrestha Y, Hu JX, Worstell E, Shea E, Ilic N, Kim E, Kamburov A, Kashani A, Hahn WC, Campbell JD, Boehm JS, Getz G, Lage K.
NetSig: network-based discovery from cancer genomes.
Nat Methods. 2018 Jan;15(1):61-66. doi: 10.1038/nmeth.4514. Epub 2017 Dec 4. PMID: 29200198; PMCID: PMC5985961.

netSmooth v0.1.0 – A Network smoothing based method for single cell RNA-seq

netSmooth v0.1.0

:: DESCRIPTION

netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using gene interaction networks such as protein- protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNA-seq data.

::DEVELOPER

Bioinformatics & Omics Data Science platform

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

netSmooth

:: MORE INFORMATION

Citation

Ronen J, Akalin A.
netSmooth: Network-smoothing based imputation for single cell RNA-seq.
F1000Res. 2018 Jan 3;7:8. doi: 10.12688/f1000research.13511.3. PMID: 29511531; PMCID: PMC5814748.

XMRF 1.0 – Fit Markov Networks to High-Throughput Genomics Data

XMRF 1.0

:: DESCRIPTION

XMRF is an R package implemented to enable biomedical researchers to discover complex interaction between genes from multi-dimensional genomics data.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

XMRF

:: MORE INFORMATION

Citation

Wan YW, Allen GI, Baker Y, Yang E, Ravikumar P, Anderson M, Liu Z.
XMRF: an R package to fit Markov Networks to high-throughput genetics data.
BMC Syst Biol. 2016 Aug 26;10 Suppl 3(Suppl 3):69. doi: 10.1186/s12918-016-0313-0. PMID: 27586041; PMCID: PMC5009817.

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