ClassifyR 1.2.4 – Performance Assessment of Classification with Applications to Transcriptomics

ClassifyR 1.2.4

:: DESCRIPTION

ClassifyR is a framework for two-class classification problems, with applications to differential variability and differential distribution testing.

::DEVELOPER

Dario Strbenac <dario.strbenac at sydney.edu.au>, John Ormerod, Graham Mann, Jean Yang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 ClassifyR

:: MORE INFORMATION

Citation

ClassifyR: An R Package for Performance Assessment of Classification with Applications to Transcriptomics.
Strbenac D, Mann GJ, Ormerod JT, Yang JY.
Bioinformatics. 2015 Feb 1. pii: btv066.

Disperse 1.0.3 – Design of Selector Assays for Targeted Resequencing Applications

Disperse 1.0.3

:: DESCRIPTION

The Disperse project aims to develop and distribute software and data for design of selector assays for exon resequencing applications. The software consists of Java and Perl code integrated into a pipeline that performs all tasks required to transform a list of gene names to a set of selector probes targetting all exonic regions of those genes

::DEVELOPER

Disperse Team

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX / Windows / Linux
  • Java
  • Perl
  • Blast

:: DOWNLOAD

 Disperse

:: MORE INFORMATION

Citation

J. Stenberg, M. Zhang and H. Ji
Disperse–a software system for design of selector probes for exon resequencing applications
Bioinformatics (2009) 25(5): 666-667

ChemDoodle 7.0.2 / ChemDoodle Mobile 1.5.0 – Chemical Drawing Application

ChemDoodle 7.0.2 / ChemDoodle Mobile 1.5.0

:: DESCRIPTION

ChemDoodle is a fully functional chemical drawing application!ChemDoodle also natively reads and writes many common file formats including ChemDraw’s CDX and CDXML. You can write ChemDraw files for submitting journal manuscripts or share these files with your rich friends who purchased ChemDraw. No longer do you need to worry if your colleages are using compatible applications or operating systems.

ChemDoodle Mobile is the mobile companion to the popular chemical publishing desktop application, ChemDoodle.

::DEVELOPER

iChemLabs

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX / IOS/ Andorid
  • Java

:: DOWNLOAD

ChemDoodle free trial , for IOS/ for Andorid

:: MORE INFORMATION

Bio-SeCo – Bioinformatics Search Computing Application

Bio-SeCo

:: DESCRIPTION

Bio-SeCo allows exploring and integrating data from external resources (e.g. NCBI and WU BLAST, Array Express, …).

::DEVELOPER

Bio-SeCo team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014;15 Suppl 1:S3. doi: 10.1186/1471-2105-15-S1-S3. Epub 2014 Jan 10.
Explorative search of distributed bio-data to answer complex biomedical questions.
Masseroli M, Picozzi M, Ghisalberti G, Ceri S.

FUNC 0.4.7 – Gene Analyzer Application

FUNC 0.4.7

:: DESCRIPTION

FUNC is a collection of four programs to analyze the over- and under-representation of data associated with genes or gene products. The test runs seperately for all three taxonomies of Gene Ontology (or the supplied root-nodes).

::DEVELOPER

Department of Genetics/Bioinformatics – Max Planck Institut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FUNC 

:: MORE INFORMATION

Citation

Kay Prüfer et al.
FUNC: a package for detecting significant associations between gene sets and ontological annotations.
BMC Bioinformatics. 2007 Feb 6;8:41.

Pebble 1.0 – Phylogenetic Analysis Application

Pebble 1.0

:: DESCRIPTION

Pebble (Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment) is a powerful application for Phylogenetic analysis. The primary purpose of Pebble is to provide tools for analysis and simulation of serially sampled sequence data (through maximum likelihood, and least-squares methods). Implemented forms of simulation include: trees, via a coalescent model, and sequence alignments, given an input tree and substitution model. Extra functionality includes data manipulation tools for sequence alignments and phylogenetic trees, as well as useful inbuilt alignment construction and editing facilities.

::DEVELOPER

the New Zealand Bioinformatics Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

 Pebble

:: MORE INFORMATION

Citation

Curr Protoc Bioinformatics. 2004 May;Chapter 6:Unit 6.8. doi: 10.1002/0471250953.bi0608s05.
Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences.
Goode M, Rodrigo AG.

GeneIndex / GeneIndexHD / GeneIndex Bacteria 1.30 – iOS Applications to Lookup Scientific Literature and Gene Information.

GeneIndex / GeneIndexHD / GeneIndex Bacteria 1.30

:: DESCRIPTION

GeneIndex / GeneIndexHD quickly provides information about genes from various sources. It also includes a RSS reader for journal feeds as well as a PubMed viewer.

In response to requests for more bacteria, GeneIndex for Bacteria contains gene info from NCBI for over 2000 strains of bacteria that each have at least 1000 genes recorded.

::DEVELOPER

Keith Ching

:: SCREENSHOTS

GeneIndex

:: REQUIREMENTS

  • iPad/iPhone

:: DOWNLOAD

 GeneIndex / GeneIndexHD / GeneIndex Bacteria

:: MORE INFORMATION

BiSSAP 1.3 – Biological Sequence Submission Application for Patents

BiSSAP 1.3

:: DESCRIPTION

BiSSAP is a computer program designed to facilitate the creation of sequence listings for patent applications containing biological sequences (see Rule 30 EPC, Rule 5.2 PCT, and the Decision of the President and Notice from the EPO dated 28 April 2011 (OJ EPO 6/2011, 372 ff.)).

::DEVELOPER

EPO BiSSAP Team (bissap@epo.org)

:: SCREENSHOTS

BiSSAP

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 BiSSAP

:: MORE INFORMATION

PD5 1.5 – Software Library for the Development of Primer Design Applications

PD5 1.5

:: DESCRIPTION

PD5 is a C++ software library of classes for the design and analysis of primers suitable for a wide range of PCR applications.

PD5 Online Version

::DEVELOPER

 the Bioinformatics group in the Department of Computer Science at Aberystwyth University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX / Linux
  • C++ Compiler

:: DOWNLOAD

 PD5

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 21;8(11):e80156. doi: 10.1371/journal.pone.0080156.
PD5: A General Purpose Library for Primer Design Software.
Riley MC, Aubrey W, Young M, Clare A.

OSCAR 6.1.1 – Open Source Cluster Application Resources

OSCAR 6.1.1

:: DESCRIPTION

OSCAR (Open Source Cluster Application Resources) is a snapshot of the best known practices for building, programming and using a cluster. The toolkit is geared towards a modest sized cluster (50+ nodes) and features a wizard-based GUI for cluster installation.

::DEVELOPER

The Open Cluster Group 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OSCAR

:: MORE INFORMATION