Freddie v0.3.1 – Long Reads Isoform Discovery Tool

Freddie v0.3.1

:: DESCRIPTION

Freddie: Annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • conda
  • Python

:: DOWNLOAD

Freddie

:: MORE INFORMATION

Citation

Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms
Baraa OrabiBrian McConeghyCedric ChauveFaraz Hach

TIPMaP – Transcript Isoform Profiles from Microarray Probes

TIPMaP

:: DESCRIPTION

TIPMaP is a tool developed to identify differentially regulated transcripts (specific to human, mouse and rat).

::DEVELOPER

Institute of Bioinformatics and Applied Biotechnology, Bangalore, India,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Chitturi N, Balagannavar G, Chandrashekar DS, Abinaya S, Srini VS, Acharya KK.
TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.
BMC Genomics. 2013 Dec 27;14:922. doi: 10.1186/1471-2164-14-922. PMID: 24373374; PMCID: PMC3884118.

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.

IUTA 1.0 – Detecting Differential Isoform usage from RNA-Seq data

IUTA 1.0

:: DESCRIPTION

IUTA (Isoform Usage Two-step Analysis) is an analysis tool of Illumina paired-end mRNA-seq data for detecting differential usage of gene transcript isoforms.

::DEVELOPER

IUTA team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

  IUTA

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Oct 6;15:862. doi: 10.1186/1471-2164-15-862.
IUTA: a tool for effectively detecting differential isoform usage from RNA-Seq data.
Niu L, Huang W, Umbach DM, Li L

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.

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

VTBuilder team

:: 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.

IDP 0.1.10/ IDP-fusion v1.1.2 – Gene Isoform Detection and Prediction tool

IDP 0.1.10 / IDP-fusion v1.1.2

:: 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.

IDP-fusion is an gene Isoform Detection and Prediction tool from Second Generation Sequencing and PacBio sequencing.

::DEVELOPER

Au Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX
  • Python

:: DOWNLOAD

 IDP / IDP-fusion

:: MORE INFORMATION

Citation

Weirather JL, Afshar PT, Clark TA, Tseng E, Powers LS, Underwood JG, Zabner J, Korlach J, Wong WH, Au KF.
Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.
Nucleic Acids Res. 2015 Oct 15;43(18):e116. doi: 10.1093/nar/gkv562. Epub 2015 Jun 3. PMID: 26040699; PMCID: PMC4605286.

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

ORMAN 1.3 – Optimal Resolution of Ambiguous RNA-Seq Multi-mappings in the Presence of Novel Isoforms

ORMAN 1.3

:: 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

Hach Lab

 

:: 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.

CEM 0.9.1 – Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads

CEM 0.9.1

:: DESCRIPTION

CEM is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 CEM

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2914-21. doi: 10.1093/bioinformatics/bts559. Epub 2012 Oct 11.
Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.
Li W1, Jiang T.

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