:: DESCRIPTION
LncDisease is a novel computational method and tool to predict the associations between lncRNAs and diseases
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
LncDisease: a sequence based bioinformatics tool for predicting lncRNA-disease associations.
Wang J, Ma R, Ma W, Chen J, Yang J, Xi Y, Cui Q.
Nucleic Acids Res. 2016 Feb 16. pii: gkw093
:: DESCRIPTION
DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Oh M, Zhang L.
DeepMicro: deep representation learning for disease prediction based on microbiome data.
Sci Rep. 2020 Apr 7;10(1):6026. doi: 10.1038/s41598-020-63159-5. PMID: 32265477; PMCID: PMC7138789.
:: DESCRIPTION
FENRIR integrates tissue-specific enhancer networks with disease GWAS or genes and reprioritizes ~48,000 enhancers.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chen X, Zhou J, Zhang R, Wong AK, Park CY, Theesfeld CL, Troyanskaya OG.
Tissue-specific enhancer functional networks for associating distal regulatory regions to disease.
Cell Syst. 2021 Mar 3:S2405-4712(21)00041-7. doi: 10.1016/j.cels.2021.02.002. Epub ahead of print. PMID: 33689683.
:: DESCRIPTION
nsSNPAnalyzer is a web tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a deleterious effect. nsSNPAnalyzer extracts structural and evolutionary information from a query nsSNP and uses a machine learning method called Random Forest to predict the nsSNP’s phenotypic effect.
::DEVELOPER
Yan Cui’s Lab at University of Tennessee Health Science Center
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W480-2.
nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.
Bao L, Zhou M, Cui Y.
:: DESCRIPTION
GS2D(Gene set to diseases) computes disease enrichment analysis on gene sets using biomedical literature data.
::DEVELOPER
Computational Biology and Data Mining (CBDM) Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Andrade-Navarro MA, Fontaine JF (2016).
Gene Set to Diseases (GS2D): Disease Enrichment Analysis on Human Gene Sets with Literature Data.
Genomics and Computational Biology, 2(1): e33.
:: DESCRIPTION
HumanNet is a human functional gene network by integrating diverse types of omics data using Bayesian statistics framework and demonstrated its ability to retrieve disease genes.
::DEVELOPER
Network Biomedicine Laboratory at Yonsei University, Korea
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
HumanNet v2: human gene networks for disease research.
Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM, Lee I.
Nucleic Acids Res. 2019 Jan 8;47(D1):D573-D580. doi: 10.1093/nar/gky1126.
:: DESCRIPTION
PEDDY is a software package to identify and facilitate the remediation of such errors via interactive visualizations and reports comparing the stated sex, relatedness, and ancestry to what is inferred from the individual genotypes derived from whole-genome (WGS) or whole-exome (WES) sequencing.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Am J Hum Genet. 2017 Mar 2;100(3):406-413. doi: 10.1016/j.ajhg.2017.01.017. Epub 2017 Feb 9.
Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy.
Pedersen BS, Quinlan AR.
:: DESCRIPTION
APSampler is a tool that allows multi-locus and multi-level association analysis of genotypic and phenotypic data. The goal is to find the allelic sets (patterns) that are associated with phenotype. The main difficulty of such a task is, given the multiple loci and multiple alleles, the number of all possible classifiers tends to be extremely large. Therefore, Monte Carlo Markov Chain method is applied to reduce the space of solutions and sample only from regions where it is likely to find a good classifier. Once a set of classifiers is found, there is a problem to validate the results, and this is done using a number of well known methods. In case of single disease level, the resulting classifier divides the space of healthy and ill individuals, and the result is represented in a classic Fisher table. Odds ratio and Fisher’s p-value are calculated if applicable. Also, Kruskal’s gamma and the corresponding p-value can be calculated. After each pattern in the output is described by a p-values set of different multiple-hypothesis corrections, including permutation tests.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Favorov, A.V. et al.
A Markov chain Monte Carlo technique for identification of combinations of allelic variants underlying complex diseases in humans.
Genetics 171, 2113-2121 (2005).
:: DESCRIPTION
WAFFECT (pronounced ‘double-u affect’ for ‘weighted affectation’) is a package to simulate phenotypic (case or control) datasets under a disease model H1 such that the total number of cases is constant across all the simulations (the constrain in the title).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hum Hered. 2012;73(2):95-104. doi: 10.1159/000336194. Epub 2012 Mar 28.
Alternative methods for H1 simulations in genome-wide association studies.
Perduca V, Sinoquet C, Mourad R, Nuel G.
:: DESCRIPTION
BEAM (Bayesian Epistasis Association Mapping) is a software for SNP-SNP interaction association mapping based on graph models, infers disease-SNP graph and automatically accounts for linkage disequilibrium.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nat Genet. 2007 Sep;39(9):1167-73. Epub 2007 Aug 26.
Bayesian inference of epistatic interactions in case-control studies.
Zhang Y, Liu JS.
