SigniSite 2.1 – Residue level Genotype Phenotype Correlation in Protein Multiple Sequence Alignments

SigniSite 2.1

:: DESCRIPTION

SigniSite performs residue level genotype phenotype correlation in protein multiple sequence alignments by identifying amino acid residues significantly associated with the phenotype of the data set.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W286-91. doi: 10.1093/nar/gkt497. Epub 2013 Jun 12.
SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.
Jessen LE1, Hoof I, Lund O, Nielsen M.

CCLasso – Correlation Inference for Compositional Data through Lasso

CCLasso

:: DESCRIPTION

CCLasso is a novel method based on least squares with ℓ1 penalty to infer the correlation network for latent variables of compositional data from metagenomic data

::DEVELOPER

Fang Huaying (hyfang@pku.edu.cn) , Minghua Deng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 CCLasso

:: MORE INFORMATION

Citation

CCLasso: Correlation Inference for Compositional Data through Lasso.
Fang H, Huang C, Zhao H, Deng M.
Bioinformatics. 2015 Jun 4. pii: btv349.

C3 – Correlation Clustering method for Cancer Mutation analysis

C3

:: DESCRIPTION

C3 (Cancer Correlation Clustering) identifies cancer mutation patterns from patient cohort by leveraging mutual exclusivity of mutations, patient coverage and driver network concentration principles.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

C3

:: MORE INFORMATION

Citation

A new correlation clustering method for cancer mutation analysis.
Hou JP, Emad A, Puleo GJ, Ma J, Milenkovic O.
Bioinformatics. 2016 Dec 15;32(24):3717-3728.

CorNet 2.01 – Correlation Network Graphs

CorNet 2.01

:: DESCRIPTION

 CorNet is a R-script largest correlation network graphs for visualizing clusters of intercorrelated genes/transcripts

::DEVELOPER

Bioinformatics at AWI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R Package

:: DOWNLOAD

 CorNet

:: MORE INFORMATION

Citation

Hüning AK, Melzner F, Thomsen J, Gutowska MA, Krämer L, Frickenhaus S, Rosenstiel P, Pörtner HO, Philipp E, Lucassen M
Impacts of seawater acidification on mantle gene expression patterns of the Baltic Sea blue mussel: implications for shell formation and energy budget. (2012),
Marine Biology . August 2013, Volume 160, Issue 8, pp 1845-1861 doi: 10.1007/s00227-012-1930-9

DICER – Differential Correlation in Expression for meta-module Recovery

DICER

:: DESCRIPTION

DICER is a tool for advanced analysis of differential co-expression (DC) case-control gene expression data.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • Java 

:: DOWNLOAD

 DICER

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2013;9(3):e1002955. doi: 10.1371/journal.pcbi.1002955. Epub 2013 Mar 7.
Dissection of regulatory networks that are altered in disease via differential co-expression.
Amar D1, Safer H, Shamir R.

CorSig – Statistical Inference of Correlation Significance

CorSig

:: DESCRIPTION

CorSig: A General Framework for Estimating Statistical Significance of Correlation and Its Application to Gene Co-expression Analysis.

::DEVELOPER

 the Tsai lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R
:: DOWNLOAD

 CorSig

:: MORE INFORMATION

Citation

PLoS One. 2013 Oct 23;8(10):e77429. doi: 10.1371/journal.pone.0077429. eCollection 2013.
CorSig: a general framework for estimating statistical significance of correlation and its application to gene co-expression analysis.
Wang HQ1, Tsai CJ.

ChIPCor 1.1.0 – Measuring the Spatial Correlations of Protein Binding Sites

ChIPCor 1.1.0

:: DESCRIPTION

ChIPCor is a testing procedure for evaluating the significance of overlapping from a pair of proteins by leveraging information from publicly available data.

::DEVELOPER

ChIPCor team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 ChIPCor

:: MORE INFORMATION

Citation:

Measuring the spatial correlations of protein binding sites.
Wei Y, Wu H.
Bioinformatics. 2016 Feb 9. pii: btw058.

MuCor – Mutation Aggregation and Correlation

MuCor

:: DESCRIPTION

MuCor is software to aggregate variant information sourced from multiple VCF files (and some others, see below) into a variety of summary files with varying levels of detail and statistics.

::DEVELOPER

blachly lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python

:: DOWNLOAD

  MuCor

:: MORE INFORMATION

Citation:

MuCor: Mutation Aggregation and Correlation.
Kroll KW, Eisfeld AK, Lozanski G, Bloomfield CD, Byrd JC, Blachly JS.
Bioinformatics. 2016 Jan 23. pii: btw028

NICE – Next-generation Intersample Correlation Emended

NICE

:: DESCRIPTION

NICE is a statistical test for correcting for expression heterogeneity inherent in expression dataset due to confounding from unmodeled factors. NICE estimates inter-sample correlation structure using only the genes with confounding effects and incorporates it as signatures of the systematic confounding effects to correct for it.

:: DEVELOPER

NICE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows /MacOsX
  • R
  • Java

:: DOWNLOAD

 NICE

:: MORE INFORMATION

Citation

Joo JW, Sul JH, Han B, Ye C, Eskin E.
Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies,
Genome Biology, 15:r61, 2014.

Correlation Finder – Seek Correlations between Nucleotides in Genomic Sequences

Correlation Finder

:: DESCRIPTION

Correlation Finder is a free software which allows to seek correlations between nucleotides in genomic sequences. It computes some parameters for each analyzed correlation: the relative abundance, the conditional probability, the frequency of the words making up the correlation.

::DEVELOPER

Gruppo di Biologia Computazionale

:: SCREENSHOTS

Correlation

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Correlation Finder

:: MORE INFORMATION

Citation:

In Silico Biol. 2005;5(5-6):465-8.
Correlation Finder.
Piva F1, Principato G.