WeiSum – Finding Genetic Overlaps among Diseases Based on Ranked Gene Lists

WeiSum

:: DESCRIPTION

WeiSum is an R package which calculates the statistics for the comparison of two ranked gene lists related to two diseases and estimates the number of potentially overlapping genes between the diseases.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R

:: DOWNLOAD

WeiSum

:: MORE INFORMATION

Citation

Quan Chen, Xianghong Jasmine Zhou, Fengzhu Sun (2015)
Finding Genetic Overlaps Among Diseases Based on Ranked Gene Lists.
In Press. Journal of Computational Biology.

MultAssoc – Test of Association of a Disease with a Group of SNPs

MultAssoc

:: DESCRIPTION

MultAssoc is a MATLAB software package for test of association of a disease with a group of SNPs after accounting for their interaction with another group of SNPs or environmental exposures. In addition to implementing two standard logistic regression based tests, the package implements a novel method, called TukAssoc, that uses the Tukey’s 1 d.f. model for interaction between two groups of covariates.

::DEVELOPER

DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Matlab

:: DOWNLOAD

MultAssoc

:: MORE INFORMATION

Citation

Chatterjee N., Kalaylioglu Z., Moslehi R., Peters U., Wacholder S. (2006).
Powerful multilocus tests of genetic association in the presence of gene-gene and gene-environment interactions.
American Journal of Human Genetics, Vol. 79, 1002-16.

TFmiR 1.2 – Disease-specific miRNA/Transcription Factor Co-regulatory Networks

TFmiR 1.2

:: DESCRIPTION

TFmiR is a freely available web server for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease pathogenesis.

::DEVELOPER

Mohamed Hamed, Christian Spaniol, Maryam Nazarieh, & Volkhard Helms, Chair of Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks.
Hamed M, Spaniol C, Nazarieh M, Helms V.
Nucleic Acids Res. 2015 May 5. pii: gkv418.

miRPD – miRNA Protein Disease Associations

miRPD

:: DESCRIPTION

miRPD is a web server in which miRNA-Protein-Disease associations are explicitly inferred.

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH), JensenLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

miRPD

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Feb 1;30(3):392-7. doi: 10.1093/bioinformatics/btt677. Epub 2013 Nov 21.
Protein-driven inference of miRNA-disease associations.
Mørk S1, Pletscher-Frankild S, Palleja Caro A, Gorodkin J, Jensen LJ.

Folding@home 7.6.21 – Understand Protein Folding, Misfolding & Related Diseases

Folding@home 7.6.21

:: DESCRIPTION

Folding@home is a distributed computing project — people from throughout the world download and run software to band together to make one of the largest supercomputers in the world. Folding@home’goal is to understand protein folding, misfolding, and related diseases

::DEVELOPER

Folding@home Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX / PlayStation3 /Android

:: DOWNLOAD

Folding@home

:: MORE INFORMATION

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.

BiRW – Reconstruct Disease Phenome-genome Association

BiRW

:: DESCRIPTION

BiRW (Bi-Random Walk)is an algorithm to capture the CBG patterns in the networks for unveiling the associations between the complete collection of disease phenotypes (phenome) and genes.

::DEVELOPER

Rui Kuang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows / MacOsX
Matlab

:: DOWNLOAD

BiRW

:: MORE INFORMATION

Citation

MaoQiang Xie, TaeHyun Hwang and Rui Kuang
Reconstructing Disease Phenome-genome Association by Bi-Random Walk
Bioinformatics (2012)doi: 10.1093/bioinformatics/bts06

MicroPattern – Microbe Set Enrichment Analysis and Disease Similarity Calculation

MicroPattern

:: DESCRIPTION

MicroPattern is a tool used to mine regular rules and patterns behind a list of microbes. MicroPattern can also be used to calculate the similarity between the given disease-associated microbe list and the collected micro-disease association dataset

::DEVELOPER

the Cui Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Ma W, Huang C, Zhou Y, Li J, Cui Q.
MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes.
Sci Rep. 2017 Jan 10;7:40200. doi: 10.1038/srep40200. PMID: 28071710; PMCID: PMC5223220.

MDCAP – MiRNA-Disease Causal Association Predictor

MDCAP

:: DESCRIPTION

The MDCAP is a computinal model for predicting novel causal miRNA-disease associations. MDCAP would calculate a score for all potential causal miRNA-disease associations. With the score, users could identify most potential causal miRNAs for a given disease or new causal associated disease of a miRNA.

::DEVELOPER

the Cui Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Windows/Linux
Python

:: DOWNLOAD

MDCAP

:: MORE INFORMATION

Citation

Gao Y, Jia K, Shi J, Zhou Y, Cui Q.
A Computational Model to Predict the Causal miRNAs for Diseases.
Front Genet. 2019 Oct 3;10:935. doi: 10.3389/fgene.2019.00935. PMID: 31632446; PMCID: PMC6786093.

DRWPClass 1.0 – Pathway-based Disease Classification

DRWPClass 1.0

:: DESCRIPTION

DRWPClass is a pathway-based disease classification method. It incorporates directed pathway topological information to infer reproducible pathway activities by directed random walk (DRW) and uses them for accurate and robust cancer classification.

::DEVELOPER

Wei Liu <freelw@gmail.com> and Chunquan Li <lcqbio@aliyun.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
R
igraph
RWeka
Matrix
lattice

:: DOWNLOAD

DRWPClass

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 1;29(17):2169-77. doi: 10.1093/bioinformatics/btt373. Epub 2013 Jul 10.
Topologically inferring risk-active pathways toward precise cancer classification by directed random walk.
Liu W1, Li C, Xu Y, Yang H, Yao Q, Han J, Shang D, Zhang C, Su F, Li X, Xiao Y, Zhang F, Dai M, Li X.