Survcomp 1.34.0 – Performance Assessment and Comparison for Survival Analysis

Survcomp 1.34.0

:: DESCRIPTION

Survcomp is an R package providing functions to assess and to compare the performance of risk prediction (survival) models.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/Bioconductor

:: DOWNLOAD

 Survcomp

:: MORE INFORMATION

Citation:

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models.
Schröder MS, Culhane AC, Quackenbush J, Haibe-Kains B.
Bioinformatics. 2011 Nov 15;27(22):3206-8. doi: 10.1093/bioinformatics/btr511.

MRMPlusGUI 20151104 – Quality Control and Assessment tool for SRM/MRM Assay development

MRMPlusGUI 20151104

:: DESCRIPTION

MRMPlusGUI is a freely available, open-source tool in the platform independent Java programming language to compute analytical measures as recommended recently by the Clinical Proteomics Tumor Analysis Consortium Assay Development Working Group for “Tier 2” assays.

::DEVELOPER

MRMPlusGUI team

:: SCREENSHOTS

MRMPlus

:: REQUIREMENTS

  • MacOsX/Linux / Windows
  • Java

:: DOWNLOAD

 MRMPlusGUI

:: MORE INFORMATION

Citation

MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development.
Aiyetan P, Thomas SN, Zhang Z, Zhang H.
BMC Bioinformatics. 2015 Dec 12;16(1):411. doi: 10.1186/s12859-015-0838-z.

BIDDSAT 0.3 – BIoDiversity DataSet Assessment Tool

BIDDSAT 0.3

:: DESCRIPTION

BIDDSAT is an online tool that enables selected diagnostic visualizations on the content of data publishers and/or their individual collections.

::DEVELOPER

Javier Otegui

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
  • PHP

:: DOWNLOAD

 BIDDSAT

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 15;28(16):2207-8. doi: 10.1093/bioinformatics/bts359. Epub 2012 Jun 23.
BIDDSAT: visualizing the content of biodiversity data publishers in the Global Biodiversity Information Facility network.
Otegui J, Ariño AH.

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.

BIGpre 2.0.2 – Quality Assessment software for both Illumina and 454 platforms

BIGpre 2.0.2

:: DESCRIPTION

BIGpre is a quality assessment package for next-genomics sequencing data

::DEVELOPER

BIGpre team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BIGpre

:: MORE INFORMATION

Citation

Genomics Proteomics Bioinformatics. 2011 Dec;9(6):238-44. doi: 10.1016/S1672-0229(11)60027-2.
BIGpre: a quality assessment package for next-generation sequencing data.
Zhang T1, Luo Y, Liu K, Pan L, Zhang B, Yu J, Hu S.

MAìSTAS – Modeling and Assessment of ISoforms Through Automated Server

MAìSTAS

:: DESCRIPTION

Maìstas is a fully automatic pipeline aimed at building and assessing three-dimensional models for alternative splicing isoforms. The server builds, when possible, comparative structural models for all the splicing isoforms of a submitted gene or set of genes. The models are then analysed in terms of their suitability to exist in the monomeric state, i.e. when a warning appears in the model assessment, it cannot be excluded the possibility that other multimeric state may stabilize the structure.

::DEVELOPER

CRS4-Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1625-9. doi: 10.1093/bioinformatics/btr198. Epub 2011 Apr 15.
MAISTAS: a tool for automatic structural evaluation of alternative splicing products.
Floris M1, Raimondo D, Leoni G, Orsini M, Marcatili P, Tramontano A.

Coala 1.2.1 – COevolution Assessment by a Likelihood-free Approach

Coala 1.2.1

:: DESCRIPTION

Coala is an algorithm for estimating the frequency of the events based on an approximate Bayesian computation approach.

::DEVELOPER

ERABLE (European Research team in Algorithms and Biology, formaL and Experimental)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Java

:: DOWNLOAD

 Coala

:: MORE INFORMATION

Citation

C. Baudet, B. Donati, B. Sinaimeri, P. Crescenzi, C. Gautier, C. Matias, and M.-F. Sagot.
Cophylogeny reconstruction via an approximate Bayesian computation.
Systematic Biology, 2014, doi:10.1093/sysbio/syu129.

T-lex 2.2.2 – Assessment of Transposable Element Presence in Next-generation Sequencing data

T-lex 2.2.2

:: DESCRIPTION

The T-lex pipeline identifies reads that indicate the presence or absence of individual TEs with high specificity. Handling a large amount of data, it can return the frequency of a TE in the population.

::DEVELOPER

The Petrov Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 T-lex

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Feb 27;43(4):e22. doi: 10.1093/nar/gku1250. Epub 2014 Dec 15.
T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data.
Fiston-Lavier AS, Barrón MG, Petrov DA, González J

Fiston-Lavier AS, Carrigan M, Petrov DA and Gonzalez J.
T-LEX: A program for fast and accurate assessment of transposable element presence using next-generation sequencing data.
Nuc. Acids. Res. 2011 Mar 1;39(6):e36. Epub 2010 Dec 21

ModFOLD 4.0 – Model Quality Assessment Server

ModFOLD 4.0

:: DESCRIPTION

The ModFOLD4 server is the latest version of server for the estimation of both the global and local (per-residue) quality of 3D protein models.

::DEVELOPER

McGuffin Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ModFOLD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W368-72. doi: 10.1093/nar/gkt294. Epub 2013 Apr 25.
The ModFOLD4 server for the quality assessment of 3D protein models.
McGuffin LJ1, Buenavista MT, Roche DB.

Sylamer 1.0 – Fast Assessment of microRNA Binding and siRNA off-target effects from Expression data

Sylamer 1.0

:: DESCRIPTION

Sylamer is a system for finding significantly over or under-represented words in sequences according to a sorted gene list. Typically it is used to find significant enrichment or depletion of microRNA or siRNA seed sequences from microarray expression data. Sylamer is extremely fast and can be applied to genome-wide datasets with ease. Results are plotted in terms of a significance landscape plot. These plots show significance profiles for each word studied across the sorted genelist.

::DEVELOPER

Enright Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java / R package / C Compiler

:: DOWNLOAD

 Sylamer

:: MORE INFORMATION

Citation

Stijn van Dongen, Cei Abreu-Goodger & Anton J. Enright;
Detecting microRNA binding and siRNA off-target effects from expression data
Nat Methods. 2008 December; 5(12): 1023–1025.