PennSeq – Isoform-specific Gene Expression Quantification in RNA-Seq

PennSeq

:: DESCRIPTION

PennSeq is a statistical method that allows each isoform to have its own non-uniform read distribution.

::DEVELOPER

Yu Hu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Perl

:: DOWNLOAD

 PennSeq

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Feb;42(3):e20. doi: 10.1093/nar/gkt1304. Epub 2013 Dec 20.
PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution.
Hu Y1, Liu Y, Mao X, Jia C, Ferguson JF, Xue C, Reilly MP, Li H, Li M.

sparseQuant 20130910 – Targeted Protein Quantification using Sparse Reference Labeling

sparseQuant 20130910

:: DESCRIPTION

sparseQuant implements a novel statistical approach for design and analysis of label-sparse selected reaction monitoring (SRM)-based targeted proteomic experiments. Label-sparse experiments strike a middle ground between the label-free and fully label-based approaches, by utilizing a reduced set of labeled reference transitions and accurately quantifying an expanded list of proteins.

::DEVELOPER

Ching-Yun (Veavi) Chang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • R package

:: DOWNLOAD

  sparseQuant

:: MORE INFORMATION

Citation

Ching-Yun Chang, Eduard Sabidó, Ruedi Aebersold, Olga Vitek.
Targeted protein quantification using sparse reference labeling
Nat Methods. 2014 Mar;11(3):301-4. doi: 10.1038/nmeth.2806

ShortStack 3.8.5 – Comprehensive Annotation and Quantification of small RNA genes

ShortStack 3.8.5

:: DESCRIPTION

ShortStack is a tool developed to process and analyze smallRNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes.

::DEVELOPER

Axtell Lab @ Penn State

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ShortStack

:: MORE INFORMATION

Citation:

Axtell MJ.
ShortStack: comprehensive annotation and quantification of small RNA genes.
RNA. 2013 Jun;19(6):740-51. doi: 10.1261/rna.035279.112. Epub 2013 Apr 22. PMID: 23610128; PMCID: PMC3683909.

XGlycScan 20140527 – Quantification of Glycosite Associated Spectra Counts

XGlycScan 20140527

:: DESCRIPTION

XGlycScan is an open-source software for N-linked glycosite assignment, quantification and quality assessment of data from mass spectrometry-based glycoproteomic analysis.

::DEVELOPER

Paul Aiyetan

:: SCREENSHOTS

XGlycScan

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 XGlycScan

:: MORE INFORMATION

Citation:

MOJ Proteom Bioinform. 2014;1(1). pii: 00004.
XGlycScan: An Open-source Software For N-linked Glycosite Assignment, Quantification and Quality Assessment of Data from Mass Spectrometry-based Glycoproteomic Analysis.
Aiyetan P1, Zhang B, Zhang Z, Zhang H.

TiQuant 2 – Biological Tissues Image Analysis and Quantification

TiQuant 2

:: DESCRIPTION

TiQuant is a modular software tool for efficient quantification of biological tissues based on volume data obtained by biomedical image modalities. It includes a number of versatile image and volume processing chains tailored to the analysis of different tissue types which have been experimentally verified. TiQuant implements a novel method for the reconstruction of three-dimensional surfaces of biological systems, data that often cannot be obtained experimentally but which is of utmost importance for tissue modelling in systems biology.

::DEVELOPER

Hoehme Lab • Research group

:: SCREENSHOTS

TiQuant

:: REQUIREMENTS

  •  Linux / WIndows /MacOsX

:: DOWNLOAD

 TiQuant

:: MORE INFORMATION

Citation

TiQuant: Software for tissue analysis, quantification and surface reconstruction.
Friebel A, Neitsch J, Johann T, Hammad S, Hengstler JG, Drasdo D, Hoehme S.
Bioinformatics. 2015 Jun 3. pii: btv346.

CircTest 0.1.0 / DCC 0.5.0 – Identification and Quantification of Circular RNAs from Sequencing Data

CircTest 0.1.0 / DCC 0.5.0

:: DESCRIPTION

CircTest tests the variation of circRNAs in respect to host genes.

DCC (detect circRNAs from chimeric reads) is a python package intended to detect and quantify circRNAs with high specificity.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R
  • Python

:: DOWNLOAD

 CircTest , DCC

:: MORE INFORMATION

Citation

Specific identification and quantification of circular RNAs from sequencing data.
Cheng J, Metge F, Dieterich C.
Bioinformatics. 2015 Nov 9. pii: btv656

FT-ARM – Identification and Quantification of Multiplexed High-resolution

FT-ARM

:: DESCRIPTION

FT-ARM (Fourier transform-all reaction monitoring) is a software package which allows you to search and quantify peptides from data acquired in a multiplexed acquisition scheme. This data is typically acquired over some defined mass window during the entire chromatogram (ex. 700-800 m/z). Presently this software supports Thermo .raw files from any high resolution platform (ex. LTQ-FT, Orbitrap). However, we plan to extend support to all instrument vendors via the Proteowizard library.

::DEVELOPER

The Bruce Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 FT-ARM

:: MORE INFORMATION

Citation

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification.
Weisbrod CR, Eng JK, Hoopmann MR, Baker T, Bruce JE.
J. Proteome Res., 2012, 11 (3), pp 1621–1632

SalmonTE 0.4 – Ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances

SalmonTE 0.4

:: DESCRIPTION

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances from Next Generation Sequencing Data.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python / R

:: DOWNLOAD

SalmonTE

:: MORE INFORMATION

Citation

Jeong HH, Yalamanchili HK, Guo C, Shulman JM, Liu Z.
An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data.
Pac Symp Biocomput. 2018;23:168-179. PMID: 29218879.

MiTie 1.0.0 – Simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples

MiTie 1.0.0

:: DESCRIPTION

MITIE (Mixed Integer Transcript IdEntification) is a software for simultaneous transcript reconstruction and quantification.

::DEVELOPER

the Biomedical Informatics Lab of Prof. Dr. Gunnar Rätsch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MiTie

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Oct 15;29(20):2529-2538.
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.
Behr J, Kahles A, Zhong Y, Sreedharan VT, Drewe P, Rätsch G.