DIAproteomics 1.2.4 – Automated Quantitative Analysis of DIA Proteomics Mass Spectrometry Measurements

DIAproteomics 1.2.4

:: DESCRIPTION

diaproteomics is a bioinformatics analysis pipeline used for quantitative processing of data independant (DIA) proteomics data.

::DEVELOPER

the Science for Life Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Docker

:: DOWNLOAD

DIAproteomics

:: MORE INFORMATION

Citation

Bichmann L, Gupta S, Rosenberger G, Kuchenbecker L, Sachsenberg T, Ewels P, Alka O, Pfeuffer J, Kohlbacher O, Röst H.
DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics.
J Proteome Res. 2021 Jul 2;20(7):3758-3766. doi: 10.1021/acs.jproteome.1c00123. Epub 2021 Jun 21. PMID: 34153189.

DanteR 0.2 – Quantitative Analysis of -omics Data

DanteR 0.2

:: DESCRIPTION

DanteR is a graphical R package that features extensive statistical and diagnostic functions for quantitative proteomics data analysis, including normalization, imputation, hypothesis testing, interactive visualization and peptide-to-protein rollup.

::DEVELOPER

Biological MS Data and Software Distribution Center , Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • R

:: DOWNLOAD

 DanteR

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):2404-6. doi: 10.1093/bioinformatics/bts449. Epub 2012 Jul 19.
DanteR: an extensible R-based tool for quantitative analysis of -omics data.
Taverner T1, Karpievitch YV, Polpitiya AD, Brown JN, Dabney AR, Anderson GA, Smith RD.

QARIP – Quantitative Analysis of Regulated Intramembrane Proteolysis

QARIP

:: DESCRIPTION

The QARIP web-server aids in the quantitative and qualitative analysis of proteomics-based regulated intramembrane proteolysis (RIP) data.

::DEVELOPER

the Dimitri Frischmann lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W459-64. doi: 10.1093/nar/gkt436. Epub 2013 May 31.
QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis.
Ivankov DN1, Bogatyreva NS, H?nigschmid P, Dislich B, Hogl S, Kuhn PH, Frishman D, Lichtenthaler SF.

quandico 1.14 – Quantitative Analysis of differences in Copy Numbers

quandico 1.14

:: DESCRIPTION

The tool quandico applies statistical methods to detect copy number variations (CNV) in a sample by comparing the read counts from next generation sequencing (NGS) performed after PCR-enrichment of regions of interest, typically a set of genes with known or expected relevance for the sample, e.g. genes that play a role in cancer. Counts from a normal control (ideally matched normal from the same individual, e.g. healthy tissue) are required.

::DEVELOPER

Frank Reinecke

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Perl

:: DOWNLOAD

 quandico

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 Jan 28;16(1):17.
Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls.
Reinecke F, Satya R, DiCarlo J.

MetaQuery 1.0.4 – Annotation and Quantitative analysis of Genes in the human Gut Microbiome

MetaQuery 1.0.4

:: DESCRIPTION

MetaQuery is a web application for rapid and quantitative analysis of specific genes in the human gut microbiome.

::DEVELOPER

Pollard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MetaQuery

:: MORE INFORMATION

Citation

MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome.
Nayfach S, Fischbach MA, Pollard KS.
Bioinformatics. 2015 Jun 22. pii: btv382.

QSVanalyser 20121206 – Quantitative Analysis of Sequence Variants

QSVanalyser 20121206

:: DESCRIPTION

QSVanalyser is a program that allows rapid, user-controlled, batchwise analysis of DNA sequence traces for estimation of the relative proportions of two sequence variants (Quantitative Sequence Variants, QSVs).

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

QSVanalyser

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 QSVanalyser

:: MORE INFORMATION

Citation

Carr IM, Robinson JI, Dimitriou R, Markham AF, Morgan AW, Bonthron DT.
Inferring relative proportions of DNA variants from sequencing electropherograms
Bioinformatics 2009 December 25:3244-3250

Schnitzcells – Quantitative Analysis of Fluorescent Time-lapse movies of Living Cells

Schnitzcells

:: DESCRIPTION

Schnitzcells is a MATLAB based software that allows for quantitative analysis of fluorescent time-lapse movies of living cells.  The software package is developed most specifically for bacteria and has been instrumental in analyzing  E.coli and B. subtilis movies.

::DEVELOPER

The Elowitz Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MabLab

:: DOWNLOAD

 Schnitzcells

:: MORE INFORMATION

Citation

Young, J. W. ,Locke, J.C.W.,Altinok,A.,Rosenfeld,N.,Bacarian,T.,Swain,P.S.,Mjolsness,E.,Alon,U.,Elowitz,M.B.
Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy.
Nature Protocols 7, 80–88 (2012)

Quantian 0.7.9.2 – Knoppix / Debian Variant Tailored to Numerical and Quantitative Analysis

Quantian 0.7.9.2

:: DESCRIPTION

Quantian (Quantian Scientific Computing Environment) is a remastering of Knoppix, the self-configuring and directly bootable cdrom/dvd that turns any pc or laptop (provided it can boot from cdrom/dvd) into a full-featured Linux workstation. Quantian also incorporates clusterKnoppix and adds support for openMosix, including remote booting of light clients in an openMosix terminal server context. Earlier releases are still available; see below for URLs for downloads as well as ordering information.

::DEVELOPER

Dirk Eddelbuettel

:: SCREENSHOTS

:: REQUIREMENTS

  • live Linux DVD ROM

:: DOWNLOAD

 Quantian

:: MORE INFORMATION

Citation:

Christopher N. Lawrence , Dirk Eddelbuettel
Quantian: A Comprehensive Statistical Computing Environment
The Political Methodologist, Volume 13, Number 2, Fall 2005