WemIQ – Isoform Quantification method for RNA-seq data

WemIQ

:: DESCRIPTION

WemIQ is a software tool to quantify isoform expression and exon splicing ratios from RNA-seq data accurately and robustly.

::DEVELOPER

Liang Chen’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 WemIQ

:: MORE INFORMATION

Citation

WemIQ: An accurate and robust isoform quantification method for RNA-seq data.
Zhang J, Kuo CC, Chen L.
Bioinformatics. 2014 Nov 17. pii: btu757.

IsoEM 2.0.0 – Inferring Alternative Splicing Isoform Frequencies from High-Throughput RNA-Seq Data

IsoEM 2.0.0

:: DESCRIPTION

IsoEM package can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. IsoEM uses a novel expectation-maximization algorithm that exploits read disambiguation information provided by the distribution of insert sizes generated during sequencing library preparation, and takes advantage of base quality scores, strand, and read pairing information (if available). Empirical experiments on synthetic datasets show that the algorithm significantly outperforms existing methods of isoform and gene expression level estimation from RNA-Seq data

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

IsoEM

:: MORE INFORMATION

Citation:

M. Nicolae and S. Mangul and I.I. Mandoiu and A. Zelikovsky,
Estimation of alternative splicing isoform frequencies from RNA-Seq data,
Algorithms for Molecular Biology , pp. to appear, 2011

Ribomap v1.2 – Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abudance

Ribomap v1.2

:: DESCRIPTION

Ribomap is a package that generates isoform-level ribosome profiles from ribosome profiling data.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • Sailfish/Salmon

:: DOWNLOAD

Ribomap

:: MORE INFORMATION

Citation

Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.
Wang H, McManus J, Kingsford C.
Bioinformatics. 2016 Jun 15;32(12):1880-2. doi: 10.1093/bioinformatics/btw085

MetaPred – Prediction of Cytochrome P450 Isoform responsible for Metabolizing a Drug Molecule

MetaPred

:: DESCRIPTION

MetaPred Server predict metabolizing CYP isoform of a drug molecule/substrate, based on SVM models developed using CDK descriptors.

::DEVELOPER

MetaPred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Pharmacol. 2010 Jul 16;10:8. doi: 10.1186/1471-2210-10-8.
Prediction of cytochrome P450 isoform responsible for metabolizing a drug molecule.
Mishra NK1, Agarwal S, Raghava GP.

NLDMseq – Expression Calculation at both Gene and Isoform levels from RNA-seq data given a Reference Transcriptom

NLDMseq

:: DESCRIPTION

NLDMseq is a bioinformatics tool for expression calculation at both gene and isoform levels from RNA-seq data by considering isoform- and exon-specific read sequencing rate.

::DEVELOPER

Xuejun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python

:: DOWNLOAD

 NLDMseq

:: MORE INFORMATION

Citation

Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate.
Liu X, Shi X, Chen C, Zhang L.
BMC Bioinformatics. 2015 Oct 16;16(1):332. doi: 10.1186/s12859-015-0750-6.

Ballgown – Isoform-level Differential Expression Analysis in R

Ballgown

:: DESCRIPTION

Ballgown is a software package designed to facilitate flexible differential expression analysis of RNA-Seq data. It also provides functions to organize, visualize, and analyze the expression measurements for your transcriptome assembly.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • R/BioCouductor

:: DOWNLOAD

 Ballgown

:: MORE INFORMATION

Citation

Nat Biotechnol. 2015 Mar;33(3):243-6. doi: 10.1038/nbt.3172.
Ballgown bridges the gap between transcriptome assembly and expression analysis.
Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT

FlipFlop 1.8.0 – Fast Lasso-based Isoform Prediction as a Flow Problem

FlipFlop 1.8.0

:: DESCRIPTION

FlipFlop is a fast method for de novo transcript discovery and abundance estimation from RNA-Seq data.

::DEVELOPER

Centre for Computational Biology

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 FlipFlop

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 9.
Efficient RNA Isoform Identification and Quantification from RNA-Seq Data with Network Flows.
Bernard E, Jacob L, Mairal J, Vert JP.

ORMAN 1.2 – Optimal Resolution of Ambiguous RNA-Seq Multi-mappings in the Presence of Novel Isoforms

ORMAN 1.2

:: DESCRIPTION

ORMAN ( Optimal Resolution of Multimapping Ambiguity of RNA-Seq Reads) is a tool for resolving multi-mappings within an RNA-Seq SAM file.

::DEVELOPER

Lab for Computational Biology at SFU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ORMAN

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 1;30(5):644-51. doi: 10.1093/bioinformatics/btt591. Epub 2013 Oct 15.
ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.
Dao P, Numanagić I, Lin YY, Hach F, Karakoc E, Donmez N, Collins C, Eichler EE, Sahinalp SC.

SERpredict – Predict Tissue or Tumor-Specific Exonised Repetitive element containing Isoforms

SERpredict

:: DESCRIPTION

SERpredict is an automated bioinformatics pipeline to predict tissue or tumor-specific repetitive element (RE)-containing isoforms in human and mouse DNA.

::DEVELOPER

HUSAR Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genet. 2007 Nov 6;8:78.
SERpredict: detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements.
Mersch B1, Sela N, Ast G, Suhai S, Hotz-Wagenblatt A.