BRB-ArrayTools 4.6.2 – Visualization & Analysis of DNA Microarray Gene Expression Data

BRB-ArrayTools 4.6.2

:: DESCRIPTION

BRB-ArrayTools is an integrated software package for the analysis of DNA microarray data.

BRB-ArrayTools contains utilities for processing expression data from multiple experiments, visualization of data, multidimensional scaling, clustering of genes and samples, and classification and prediction of samples. BRB-ArrayTools features drill-down linkage to NCBI databases using clone, GenBank, or UniGene identifiers, and drill-down linkage to the NetAffx database using Probeset ids.

::DEVELOPER

the Biometric Research Branch of the Division of Cancer Treatment & Diagnosis of the National Cancer Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

BRB-ArrayTools

:: MORE INFORMATION

Citation

Analysis of gene expression data using BRB-ArrayTools.
Simon R, Lam A, Li MC, Ngan M, Menenzes S, Zhao Y.
Cancer Inform. 2007 Feb 4;3:11-7.

XMRF 1.0 – Fit Markov Networks to High-Throughput Genomics Data

XMRF 1.0

:: DESCRIPTION

XMRF is an R package implemented to enable biomedical researchers to discover complex interaction between genes from multi-dimensional genomics data.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

XMRF

:: MORE INFORMATION

Citation

Wan YW, Allen GI, Baker Y, Yang E, Ravikumar P, Anderson M, Liu Z.
XMRF: an R package to fit Markov Networks to high-throughput genetics data.
BMC Syst Biol. 2016 Aug 26;10 Suppl 3(Suppl 3):69. doi: 10.1186/s12918-016-0313-0. PMID: 27586041; PMCID: PMC5009817.

Paxtools 5.1.0 / PaxtoolsR 1.26.0 – Accessing & Manipulating BioPAX Data

Paxtools 5.1.0 / PaxtoolsR 1.26.0

:: DESCRIPTION

Paxtools is a Java library specially designed for accessing and manipulating data in BioPAX format. The Paxtools Java programming library for BioPAX has been developed to help software developers readily support the import, export and validation of BioPAX-formatted data for various uses in their software . Using Paxtools, a range of BioPAX-compatible software has been developed, including browsers, visualizers, querying engines, editors and converters

PaxtoolsR provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database that are hosted by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC).

::DEVELOPER

Computational Biology Center at MSKCC 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java / R/ BioConductor

:: DOWNLOAD

 Paxtools , PaxtoolsR

:: MORE INFORMATION

Citation:

PaxtoolsR: Pathway Analysis in R Using Pathway Commons.
Luna A, Babur Ö, Aksoy BA, Demir E, Sander C.
Bioinformatics. 2015 Dec 18. pii: btv733.

Demir et al.
The BioPAX community standard for pathway data sharing
Nature Biotechnology 28 , 935–942 (2010) doi:10.1038/nbt.1666

QUALIFIER 1.26.1 – Qualitiy Control for Gated Flow Cytometry data

QUALIFIER 1.26.1

:: DESCRIPTION

The QUAliFiER package takes advantage of the manual gates to perform an extensive series of statistical quality assessment checks on the gated cell sub-populations while taking into account the structure of the data and the study design to monitor the consistency of population statistics across staining panels, subject, aliquots, channels, or other experimental variables.

::DEVELOPER

Raphael Gottardo’s Research Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX /Windows
  • R package
  • BioConductor

:: DOWNLOAD

 QUALIFIER

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 28;13:252. doi: 10.1186/1471-2105-13-252.
QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data.
Finak G, Jiang W, Pardo J, Asare A, Gottardo R.

FISH Oracle 2 – Visualize Data from multiple Array CGH or SNP Array Experiments

FISH Oracle 2

:: DESCRIPTION

FISH Oracle is a web-based software to visualize data from multiple array CGH or SNP array experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (like gene names or karyobands), quick navigation and  zooming into interesting regions, and mechanisms to export the visualization into different high quality image formats (PDF, PS, PNG, SVG).

::DEVELOPER

RESEARCH GROUP FOR GENOME INFORMATICS ,Center for Bioinformatics, University of Hamburg

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX
  • MySQL
  • Java
  • Apache Tomcat server
  • GenomeTools

:: DOWNLOAD

  FISH Oracle

:: MORE INFORMATION

Citation

M. Mader, R. Simon, S. Steinbiss and S. Kurtz:
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.
Journal of Clinical Bioinformatics, 1:20 (2011)

cMonkey 2 1.2.2 – Biclustering from Diverse System Biology Data

cMonkey 2 1.2.2

:: DESCRIPTION

cMonkey identifies relevant conditions in which the genes within a given bicluster (where “biclustering” is condition- or cell-state-specific clustering) are expected to be co-regulated (importantly, in later stages of analysis we use only these conditions to learn TFs and EFs that influence each bicluster). The methods separates the calculation of the score components associated with each datatype into individual calculations but still effectively sample biclusters that optimally satisfy multiple model components (each representing a separate data-type). The method was designed as a preprocessing step for network inference and performed well in comparison to all other methods tested when the trade-off between sensitivity, specificity, and coverage (fraction of conditions and genes included in one or more biclusters) were considered, particularly in context of the other bulk characteristics (cluster size, residual, etc.).

::DEVELOPER

Baliga Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

cMonkey

:: MORE INFORMATION

Citation

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.
Reiss DJ, Plaisier CL, Wu WJ, Baliga NS.
Nucleic Acids Res. 2015 Apr 14. pii: gkv300.

BMC Bioinformatics. 2006 Jun 2;7:280.
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks.
Reiss DJ, Baliga NS, Bonneau R.

MitoSeek 1.3 – Extract Mitochondrial Genome information from Exome Sequencing data

MitoSeek 1.3

:: DESCRIPTION

MitoSeek is an open-source software tool to reliably and easily extract mitochondrial genome information from exome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers, and detects heteroplasmy, somatic mutation, and structural variance of the mitochondrial genome.

::DEVELOPER

Jiang (River) Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MitoSeek

:: MORE INFORMATION

Citation

Yan Guo, Jiang Li, Yu Shyr, David C. Samuels.
MitoSeek: Extracting Mitochondria Information and Performing High Throughput Mitochondria Sequencing Analysis.
Bioinformatics (2013) 29 (9): 1210-1211

BLISS 0.7 – Identify Batch Effects in RNA Expression Data

BLISS 0.7

:: DESCRIPTION

BLISS (The Batch anaLysIS Suite) is intended to help identify batch effects in RNA expression data.  It has been tested on miRNA and mRNA results derived from the illumina sequencing platform.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 BLISS

:: MORE INFORMATION

eRNA 1.01 – RNA Data Analysis Tool

eRNA 1.01

:: DESCRIPTION

eRNA is an RNA data analysis tool for high-throughput RNA sequencing experiments

::DEVELOPER

eRNA team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • Perl
  • R

:: DOWNLOAD

 eRNA 

:: MORE INFORMATION

Citation:

BMC Genomics. 2014 Mar 5;15:176. doi: 10.1186/1471-2164-15-176.
eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.
Yuan T, Huang X, Dittmar RL, Du M, Kohli M, Boardman L, Thibodeau SN, Wang L

BioAnalyzer 2100 – Analysis of BioAnalyzer data

BioAnalyzer 2100

:: DESCRIPTION

The Agilent 2100 BioAnalyzer is a nanofluidics device that preforms size fractionation and quantification of small samples of DNA, RNA, or Protein. In addition, the BioAnalyzer is able to preform flow cytometry on small numbers of cells.

::DEVELOPER

the MIT BioMicro Center

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BioAnalyzer

:: MORE INFORMATION