RIscoper – RNA Interaction Extraction from Literatures

RIscoper

:: DESCRIPTION

RIscoper (RNA Interactome Scoper) represents the first tool for full-scale RNA interactome scanning and was developed for extracting RRIs from the literature based on the N-gram model.

::DEVELOPER

WD Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

RIscoper

:: MORE INFORMATION

Citation

Zhang Y, Liu T, Chen L, Yang J, Yin J, Zhang Y, Yun Z, Xu H, Ning L, Guo F, Jiang Y, Lin H, Wang D, Huang Y, Huang J.
RIscoper: a tool for RNA-RNA interaction extraction from the literature.
Bioinformatics. 2019 Sep 1;35(17):3199-3202. doi: 10.1093/bioinformatics/btz044. PMID: 30668649.

DPPI – Convolutional Neural network to predict PPI Interactions

DPPI

:: DESCRIPTION

DPPI uses a convolutional neural network to predict PPI interactions by using only the protein sequences.

::DEVELOPER

Somaye Hashemifar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DPPI

:: MORE INFORMATION

Citation:

Hashemifar S, Neyshabur B, Khan AA, Xu J.
Predicting protein-protein interactions through sequence-based deep learning.
Bioinformatics. 2018 Sep 1;34(17):i802-i810. doi: 10.1093/bioinformatics/bty573. PMID: 30423091; PMCID: PMC6129267.

NIpredict – Nuclear Import Activity Predictor based on NLS-import Receptor Interaction

NIpredict

:: DESCRIPTION

NIpredict is a method to predict nuclear import activity based on characterization of NLS-import receptor interaction using molecular interaction energy components (MIECs).

::DEVELOPER

Machine Learning and Evolution Laboratory (MLEG)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Proteins. 2014 Oct;82(10):2783-96. doi: 10.1002/prot.24642. Epub 2014 Jul 31.
Computational identification of post-translational modification-based nuclear import regulations by characterizing nuclear localization signal-import receptor interaction.
Lin JR1, Liu Z, Hu J.

powerGWASinteraction 1.1.3 – Power Calculations for Interactions for GWAS

powerGWASinteraction 1.1.3

:: DESCRIPTION

power GWAS interaction is the code for approximate power calculations for identification of gene x gene and gene x environment interactions in genomewide association studies using a two-stage analysis.

::DEVELOPER

Charles Kooperberg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  powerGWASinteraction

:: MORE INFORMATION

Citation

C. Kooperberg and M. LeBlanc (2008).
Increasing the power of identifying gene x gene interactions in genome-wide association studies
Genetic Epidemiology, 32, 255-263.

Cancerin – Infer Competing Endogenous RNA (ceRNA) interactions in Cancer

Cancerin

:: DESCRIPTION

Cancerin is a tool to infer genome-wide cancer-associated ceRNA interaction network in cancer.

::DEVELOPER

Bozdag Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

Cancerin

:: MORE INFORMATION

Citation

Do D, Bozdag S.
Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks.
PLoS Comput Biol. 2018 Jul 16;14(7):e1006318. doi: 10.1371/journal.pcbi.1006318. PMID: 30011266; PMCID: PMC6072113.

PathwaysWeb 2.0 – Gene Pathways API with Directional Interactions, Expanded Gene Ontology, and Versioning

PathwaysWeb 2.0

:: DESCRIPTION

PathwaysWeb provides publicly available information on genes, biological pathways, Gene Ontology terms, gene gene interaction networks with interaction directionality, and links to related PubMed documents.

::DEVELOPER

PathwaysWeb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PathwaysWeb: A Gene Pathways API with Directional Interactions, Expanded Gene Ontology, and Versioning.
Melott JM, Weinstein JN, Broom BM.
Bioinformatics. 2015 Sep 23. pii: btv554.

multiMiR 1.0.1 – Integration of microRNA-target Interactions along with their Disease and Drug Associations

multiMiR 1.0.1

:: DESCRIPTION

The R package multiMiR is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs.

::DEVELOPER

Yuanbin Ru at Windber Research Institute & Katerina Kechris at the University of Colorado Denver.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 multiMiR

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014;42(17):e133. doi: 10.1093/nar/gku631. Epub 2014 Jul 24.
The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations.
Ru Y, Kechris KJ, Tabakoff B, Hoffman P, Radcliffe RA, Bowler R, Mahaffey S, Rossi S, Calin GA, Bemis L, Theodorescu D.

GenomicInteractions 1.26.0 – Exploring Chromatin interaction data

GenomicInteractions 1.26.0

:: DESCRIPTION

GenomicInteractions is an R/Bioconductor package for manipulating and investigating chromatin interaction data.

::DEVELOPER

Computational Regulatory Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows  / MacOsX
  • R/Bioconductor

:: DOWNLOAD

GenomicInteractions

:: MORE INFORMATION

Citation:

Harmston N, Ing-Simmons E, Perry M, Barešić A, Lenhard B.
GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data.
BMC Genomics. 2015 Nov 17;16:963. doi: 10.1186/s12864-015-2140-x. PMID: 26576536; PMCID: PMC4650858.

PLIC – Protein-ligand Interaction Clusters

PLIC

:: DESCRIPTION

PLIC is a database of protein-ligand interaction clusters.

::DEVELOPER

Chandra lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Anand P, Nagarajan D, Mukherjee S, Chandra N.
PLIC: protein-ligand interaction clusters.
Database (Oxford). 2014 Apr 23;2014(0):bau029. doi: 10.1093/database/bau029. PMID: 24763918; PMCID: PMC3998096.

MTide – Identification of miRNA-target Interaction in Plants

MTide

:: DESCRIPTION

MTide is an integrated tool for the identification of miRNA-target interaction in plants. The core algorithm consists of a modified miRDeep2 and a modified CleaveLand4.

::DEVELOPER

Ming Chen’s Bioinformatics Group, Zhejiang University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MTide

:: MORE INFORMATION

Citation

MTide: an integrated tool for the identification of miRNA-target interaction in plants.
Zhang Z, Jiang L, Wang J, Chen M.
Bioinformatics. 2014 Sep 24. pii: btu633.