QUBIC2 / QUBIC-R 1.20.1 – Biclustering Tool for Microarray Data

QUBIC2 / QUBIC-R 1.20.1

:: DESCRIPTION

QUBIC ( QUalitative BIClustering algorithm) provides a biclustering module for microarray data. For a set of genes and a set of conditions, the program outputs a block-like structure which shows uniform pattern within the block, the block would contain only subsets of all given genes under subsets of all given conditions.

QUBIC2 is a novel biclustering algorithm for analyses of gene expression data from bulk and single-cell RNA-Sequencing.

::DEVELOPER

Qin Ma  , Bioinformatic and Mathematical Biosciences Lab, The Ohio State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

QUBIC2 / QUBIC-R

:: MORE INFORMATION

Citation

Zhang Y, Xie J, Yang J, Fennell A, Zhang C, Ma Q.
QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data.
Bioinformatics. 2017 Feb 1;33(3):450-452. doi: 10.1093/bioinformatics/btw635. PMID: 28172469.

Guojun Li, Qin Ma, Haibao Tang, Andrew H. Paterson, Ying Xu,
QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene Expression Data,
Nucleic Acids Research, 2009, 37(15): e101-

QCanvas 1.2.1 – Fast Clustering and Visualization of data

QCanvas 1.2.1

:: DESCRIPTION

QCanvas integrates diverse clustering algorithms and an interactive heatmap display interface. It directly imports raw experimental data in a matrix format and displays these data in a heatmap.

::DEVELOPER

Lab of Bioinformatics and Molecular Design

:: SCREENSHOTS

Qcanvas

:: REQUIREMENTS

  • Windows
  • Java

:: DOWNLOAD

 QCanvas

:: MORE INFORMATION

Citation

Genomics Inform. 2012 Dec;10(4):263-5. doi: 10.5808/GI.2012.10.4.263.
QCanvas: An Advanced Tool for Data Clustering and Visualization of Genomics Data.
Kim N, Park H, He N, Lee HY, Yoon S.

CAFS 1.0 – Cluster of Functional Shifts

CAFS 1.0

:: DESCRIPTION

CAFS (Clustering Analysis of Functional Shifts / Clusterfunc) is a simple and fast method for Clustering functionally divergent genes by Functional Category. The program analyses alignments and provides the user with the best putative sites under functional divergence.

::DEVELOPER

Dr Mario Fares 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 CAFS

:: MORE INFORMATION

Citation

Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, et al. (2012)
Proteome-wide analysis of functional divergence reveals the molecular basis of ecological adaptations in bacteria .
PLoS ONE 7(4): e35659. doi:10.1371/journal.pone.0035659

AptaCluster / AptaGUI – Efficient Clustering of HT-SELEX Aptamer Pools

AptaCluster / AptaGUI

:: DESCRIPTION

AptaCluster allows for an efficient clustering of whole HT-SELEX aptamer pools; a task that could not be accomplished with traditional clustering algorithms due to the enormous size of such datasets

AptaGUI is a graphical user interface for AptaCluster, written in Java. This program allows for visual inspection of HT-SELEX experiments in a concise and efficient manner.

::DEVELOPER

Teresa Przytycka Research Group

:: SCREENSHOTS

AptaGUI

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Java

:: DOWNLOAD

 AptaCluster / AptaGUI

:: MORE INFORMATION

Citation:

AptaCluster – A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application.
Hoinka J, Berezhnoy A, Sauna ZE, Gilboa E, Przytycka TM.
Research in Computational Molecular Biology Lecture Notes in Computer Science Volume 8394, 2014, pp 115-128

Cluster 3.0 20190830 – Enhanced Version of Cluster

Cluster 3.0 20190830

:: DESCRIPTION

Cluster 3.0 is an enhanced version of Cluster, which was originally developed by Michael Eisen while at Stanford University.

Cluster is program that provide a computational and graphical environment for analyzing data from DNA microarray experiments, or other genomic datasets. The program Cluster can organize and analyze the data in a number of different ways.

The main improvement consists of the k-means algorithm, which now includes multiple trials to find the best clustering solution. This is crucial for the k-means algorithm to be reliable.The routine for self-organizing maps was extended to include 2D rectangular geometries. The Euclidean distance and the city-block distance were added to the available measures of similarity.

::DEVELOPER

Michiel de Hoon of the University of Tokyo

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Mac OS X
  • Linux/Unix with Motif

:: DOWNLOAD

Cluster 

:: MORE INFORMATION

Reference: M. J. L. de Hoon, S. Imoto, J. Nolan, and S. Miyano:
Open Source Clustering Software.
Bioinformatics20 (9): 1453–1454 (2004).

Bicluster – Seed-based Biclustering of Gene Expression Data

Bicluster

:: DESCRIPTION

Bicluster is a seed-based algorithm that identifies coherent genes in an exhaustive, but efficient manner.

::DEVELOPER

AUSTRALIAN PROSTATE CANCER RESEARCH CENTRE.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  •  java

:: DOWNLOAD

 Bicluster

:: MORE INFORMATION

Citation

An J, Liew AW-C, Nelson CC (2012)
Seed-Based Biclustering of Gene Expression Data.
PLoS ONE 7(8): e42431. doi:10.1371/journal.pone.0042431

piClust – Find piRNA Clusters and Transcripts from small RNA-seq data

piClust

:: DESCRIPTION

piClust uses a density based clustering approach without assumption of any parametric distribution to improve piRNA cluster identification.

::DEVELOPER

B&H Lab, Sun Kim group, Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

piClust: a density based piRNA clustering algorithm.
Jung I, Park JC, Kim S.
Comput Biol Chem. 2014 Jun;50:60-7. doi: 10.1016/j.compbiolchem.2014.01.008.

MCL 14-137 / MCL-edge – Cluster Algorithm for Graphs

MCL 14-137 / MCL-edge

:: DESCRIPTION

MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.

MCL-edge is a set of ready-made network analysis tools (including MCL) that are single-mindedly focussed at analysis of very large networks, scaling up to millions of nodes and hundreds of millions of edges.

::DEVELOPER

Stijn Van Dongen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MCL , MCL-edge 

:: MORE INFORMATION

Citation:

Stijn Van Dongen
Graph clustering via a discrete uncoupling process.
Siam Journal on Matrix Analysis and Applications 30-1, p121-141, 2008.

CLOSET r78 – CLoud Open SequencE clusTering

CLOSET r78

:: DESCRIPTION

CLOSET is a map-reduce framework for clustering sequences from metagenomic samples, such as 454 reads.

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • HADOOP cluster

:: DOWNLOAD

  CLOSET

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2013 Feb;11(1):1340001. doi: 10.1142/S0219720013400015. Epub 2012 Dec 25.
Large-scale metagenomic sequence clustering on map-reduce clusters.
Yang X1, Zola J, Aluru S.

HTSCluster 2.0.8 – Clustering High Throughput Sequencing (HTS) data

HTSCluster 2.0.8

:: DESCRIPTION

HTSCluster implements a Poisson mixture model to cluster observations (e.g., genes) in high throughput sequencing data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).

::DEVELOPER

Andrea Rau <andrea.rau at jouy.inra.fr>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R

:: DOWNLOAD

 HTSCluster

:: MORE INFORMATION

Citation:

Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models.
Rau A, Maugis-Rabusseau C, Martin-Magniette ML, Celeux G.
Bioinformatics. 2015 Jan 5. pii: btu845.