Tag: Quantify

EMSAR v2.0.1 – Quantify Transcripts from RNA-seq data

EMSAR v2.0.1

:: DESCRIPTION

EMSAR (Estimation by Mappability-based Segmentation And Reclustering) is a new approach for quantifying transcript abundance from RNA-seq data.The software groups reads according to the set of transcripts to which they are mapped and finds maximum likelihood estimates using a joint Poisson model for each optimal set of segments of transcripts.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  EMSAR

:: MORE INFORMATION

Citation

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.
Lee S, Seo CH, Alver BH, Lee S, Park PJ.
BMC Bioinformatics. 2015 Sep 3;16(1):278. doi: 10.1186/s12859-015-0704-z.

FiloDetect – Detect & Quantify Filopodia in Single-cell Fluorescence Confocal Microscopy Images

FiloDetect

:: DESCRIPTION

FiloDetect is an image analysis program for detecting and quantifying filopodia in single-cell fluorescence confocal microscopy images.

::DEVELOPER

Perkins Lab at the OHRI

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX /Windows
  •  MatLab

:: DOWNLOAD

 FiloDetect

:: MORE INFORMATION

Citation

S. Nilufar, A. A. Morrow, J. M. Lee, T. J. Perkins
“FiloDetect: Automatic Detection of Filopodia from Fluorescence Microscopy Images”
BMC Syst Biol. 2013 Jul 23;7:66. doi: 10.1186/1752-0509-7-66.

QuasR 1.32.0 – Quantify and Annotate Short Reads in R

QuasR 1.32.0

:: DESCRIPTION

QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification.

::DEVELOPER

Anita Lerch, Dimos Gaiditzis and Michael Stadler <michael.stadler at fmi.ch>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 QuasR

:: MORE INFORMATION

Citaton

QuasR: Quantification and annotation of short reads in R.
Gaidatzis D, Lerch A, Hahne F, Stadler MB.
Bioinformatics. 2014 Nov 21. pii: btu781.

MapDamage 2.2.1 – Identifies and Quantifies DNA Damage Patterns in Ancient DNA

MapDamage 2.2.1

:: DESCRIPTION

mapDamage is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

::DEVELOPER

The Centre for Anthropobiology and Genomics of Toulouse

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Python
  • R package

:: DOWNLOAD

 MapDamage

:: MORE INFORMATION

Citation

Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L.
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.
Bioinformatics (2013) 29 (13): 1682-1684. doi: 10.1093/bioinformatics/btt193

MALDIPepQuant 3.1 – Quantify MALDI peptides (SILAC) from Phenyx output

MALDIPepQuant 3.1

:: DESCRIPTION

MALDIPepQuant is a tool to quantify MALDI peptides (SILAC) from Phenyx  output

::DEVELOPER

Swiss Institute of Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Java

:: DOWNLOAD

 MALDIPepQuant

:: MORE INFORMATION

Citation

Coute Y., Hernandez C., Appel R. D., Sanchez J.-C., Margolles A. 2007.
Labeling of Bifidobacterium longum Cells with 13C-Substituted Leucine for Quantitative Proteomic Analyses.
Appl. Environ. Microbiol. 2007 Sep;73(17):5653-6. Epub 2007 Jun 29

MFPaQ 4.0.0 – Parse, Validate, and Quantify MS Proteomics Data

MFPaQ 4.0.0

:: DESCRIPTION

MFPaQ (Mascot File Parsing and Quantification ) is a new web application dedicated to parse, validate, and quantify proteomics data. It allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).

::DEVELOPER

the MFPaQ developper

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsx
  • Firefox 2 or higher
  • Mascot server 2.1 or higher
  • Apache
  • Perl

:: DOWNLOAD

 MFPaQ

:: MORE INFORMATION

Citation

Bouyssié D, Gonzalez de Peredo A, Mouton E, Albigot R, Roussel L, Ortega N, Cayrol C, Burlet-Schiltz O, Girard J-P, and Monsarrat B.
MFPaQ, a new software to parse, validate, and quantify proteomic data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomic study of membrane proteins from primary human endothelial cells
Molecular & Cellular Proteomics, 6, 1621-1637

QUMA 1.1.13 – Visualize and Quantify Bisulfite Sequence data for CpG Methylation Analysis

QUMA 1.1.13

:: DESCRIPTION

QUMA （QUantification tool for Methylation Analysis）is a web-based tool for CpG methylation analysis.Youcan easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis

::DEVELOPER

Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 QUMA

:: MORE INFORMATION

Citation

Yuichi Kumaki, Masaaki Oda & Masaki Okano
QUMA: quantification tool for methylation analysis
Nucleic Acids Res. 36, W170-W175 (2008).