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.

Community-Analyzer – Microbiome Community Network Analysis

Community-Analyzer

:: DESCRIPTION

Community Analyzer is a GUI based Comparative Metagenomic Analysis platform that can be used to perform interactive ‘on the fly’ analysis of a given set of metagenomes on a PC/laptop with modest hardware configurations.

::DEVELOPER

Community-Analyzer team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

Community Analyzer

:: MORE INFORMATION

Citation

Kuntal BK, Ghosh TS, Mande SS.
Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes.
Genomics. 2013 Oct;102(4):409-18. doi: 10.1016/j.ygeno.2013.08.004. Epub 2013 Aug 24. PMID: 23978768.

FNV 1.0 – Light-weight Flash-based Network and Pathway Viewer

FNV 1.0

:: DESCRIPTION

FNV (Flashed-based Network Viewer) is for the visualization of small to moderately sized biological networks and pathways. FVN can also be used to embed pathways inside PDF files for the communication of pathways in soft publication materials

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

FNV

:: REQUIREMENTS

  • Windows/Linux
  • Flash Player 

:: DOWNLOAD

 FNV

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 15;27(8):1181-2. doi: 10.1093/bioinformatics/btr098. Epub 2011 Feb 23.
FNV: light-weight flash-based network and pathway viewer.
Dannenfelser R, Lachmann A, Szenk M, Ma’ayan A.

canEvolve – Integrative Cancer Genomics analysis of Expression, Copy Number, miRNAs and Network

canEvolve

:: DESCRIPTION

canEvolve query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. canEvolve stores gene, microRNA (miRNA) and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information. canEvolve allows querying of results of primary analysis, integrative analysis and network analysis of oncogenomics data. The querying for primary analysis includes differential gene and miRNA expression as well as changes in gene copy number measured with SNP microarrays. At present canEvolve provides different types of information extracted from 90 cancer genomics studies comprising of more than 10,000 patients. The presence of multiple data types, novel integrative analysis for identifying regulators of oncogenesis, network analysis and ability to query gene lists/pathways are distinctive features of canEvolve. canEvolve will facilitate integrative and meta-analysis of oncogenomics datasets.

::DEVELOPER

CanEvolve Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

canEvolve: a web portal for integrative oncogenomics.
Samur MK, Yan Z, Wang X, Cao Q, Munshi NC, Li C, Shah PK.
PLoS One. 2013;8(2):e56228. doi: 10.1371/journal.pone.0056228.

OrthoClust – Orthology-based Network Framework for Clustering data across multiple Species

OrthoClust

:: DESCRIPTION

OrthoClust is a clustering algorithm built on a multilayer network framework. It concatenates networks from individual species by their orthology relationships, arriving at a multiplex network. By optimizing the a generalized modularity function, OrthoClust returns a set of modules that could be either conserved or species-specific.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

OrthoClust

:: MORE INFORMATION

Citation:

Genome Biol. 2014 Aug 28;15(8):R100. doi: 10.1186/gb-2014-15-8-r100.
OrthoClust: an orthology-based network framework for clustering data across multiple species.
Yan KK, Wang D, Rozowsky J, Zheng H, Cheng C, Gerstein M.

PubNet – Publication Network Graph Utility

PubNet

:: DESCRIPTION

 PubNet is a utility that extracts several types of relationships returned by PubMed queries and maps them into networks, allowing for graphical visualization, textual navigation, and topological analysis. PubNet supports the creation of complex networks derived from the contents of individual citations, such as genes, proteins, Protein Data Bank (PDB) IDs, Medical Subject Headings (MeSH) terms, and authors.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

PubNet: a flexible system for visualizing literature derived networks.
SM Douglas, GT Montelione, M Gerstein (2005).
Genome Biol 6:R80.

NetAutoProbit – Network Auto-Probit Modeling for Binary Network Processes

NetAutoProbit

:: DESCRIPTION

NetAutoProbit is a matlab software of network-based auto-probit method for protein function prediction.

::DEVELOPER

Eric D. Kolaczyk

:: SCREENSHOTS

n/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Matlab

:: DOWNLOAD

 NetAutoProbit

:: MORE INFORMATION

Citation

Biometrics. 2011 Sep;67(3):958-66. doi: 10.1111/j.1541-0420.2010.01519.x. Epub 2010 Dec 6.
Network-based auto-probit modeling for protein function prediction.
Jiang X, Gold D, Kolaczyk ED.

CrossTalkZ 1.4 – Statistical tool to assess Crosstalk Enrichment between Node Groupings in a Network

CrossTalkZ 1.4

:: DESCRIPTION

CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks.

:: DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

 CrossTalkZ

:: MORE INFORMATION

Citation

PLoS One. 2013;8(1):e54945. doi: 10.1371/journal.pone.0054945. Epub 2013 Jan 23.
Statistical assessment of crosstalk enrichment between gene groups in biological networks.
McCormack T, Frings O, Alexeyenko A, Sonnhammer EL.