ModFOLD 6 – Model Quality Assessment Server

ModFOLD 6

:: DESCRIPTION

The ModFOLD 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

Maghrabi, A.H.A. & McGuffin, L.J. (2017)
ModFOLD6: an accurate web server for the global and local quality estimation of 3D models of proteins,
Nucleic Acids Res. 2017 Jul 3;45(W1):W416-W421. doi: 10.1093/nar/gkx332.

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.

NVT 1.0 – R package for the Assessment of RNA-Seq Normalization methods

NVT 1.0

:: DESCRIPTION

NVT (NORMALIZATION VISUALIZATION TOOL) is an R package for the assessment of RNA-Seq normalization methods.

::DEVELOPER

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

NVT

:: MORE INFORMATION

Citation:

Bioinformatics, 32 (23), 3682-3684 2016 Dec 1
NVT: A Fast and Simple Tool for the Assessment of RNA-seq Normalization Strategies
Thomas Eder, Florian Grebien, Thomas Rattei

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

MAìSTAS team

:: 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.

mRIN 1.2.0 – direct Assessment of mRNA integrity from RNA-Seq data

mRIN 1.2.0

:: DESCRIPTION

mRIN (mRNA integrity number) is a computational method to assess a quantitative measure of mRNA integrityta. This is done by quantitatively modeling of the 3′ bias of read coverage profiles along each mRNA transcript. A per-sample summary mRIN is then derived as an indicator of mRNA degradation. This method has been used for systematic analysis of large scale RNA-Seq data of postmortem tissues, in which RNA degradation during tissue collection is particularly an issue.

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl 

:: DOWNLOAD

mRIN

:: MORE INFORMATION

Citation

Nat Commun. 2015 Aug 3;6:7816. doi: 10.1038/ncomms8816.
mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data.
Feng H, Zhang X, Zhang C

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

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.