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.

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.

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.

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.

IDP 0.1.8 – Gene Isoform Detection and Prediction tool

IDP 0.1.8

:: DESCRIPTION

IDP is an gene Isoform Detection and Prediction tool from Second Generation Sequencing and PacBio sequencing. It offers very reliable gene isoform identification with high sensitivity.

::DEVELOPER

Kin Fai Au

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX
  • Python

:: DOWNLOAD

 IDP

:: MORE INFORMATION

Citation

Kin Fai Au, Vittorio Sebastiano, Pegah Tootoonchi Afshar, Jens Durruthy Durruthy, Lawrence Lee, Brian A. Williams, Honoratus Van Bakel, Eric Schadt, Renee A. Reijo Pera, Jason Underwood, Wing Hung Wong
Characterization of the human ESC transcriptome by hybrid sequencing
Proc. Natl. Acad. Sci. USA 2013 110 (50) E4821-E4830

VTBuilder – Assembly of Multi Isoform Transcriptomes

VTBuilder

:: DESCRIPTION

VTBuilder is a tool for the inference of non-chimeric contigs from read data that has been sequenced from complex multi-isoformic transcriptomes, such as snake venom glands, or rapidly evolving viral populations, such as HIV-1.

::DEVELOPER

John Archer and Simon Wagstaff

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • JRE

:: DOWNLOAD

 VTBuilder

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Dec 3;15(1):389.
VTBuilder: a tool for the assembly of multi isoform transcriptomes.
Archer JP, Whiteley G, Casewell NR, Harrison RA, Wagstaff SC.

rSeqDiff 0.1 – Detecting differential Isoform Expression from RNA-seq data

rSeqDiff 0.1

:: DESCRIPTION

rSeqDiff is an R package that can detect differential gene and isoform expressions from RNA-seq data of multiple biological conditions.

::DEVELOPER

Hui Jiang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 rSeqDiff

:: MORE INFORMATION

Citation:

PLoS One. 2013 Nov 18;8(11):e79448. doi: 10.1371/journal.pone.0079448. eCollection 2013.
rSeqDiff: detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test.
Shi Y1, Jiang H.