Net-RSTQ – Network-based method for RNA-Seq-based Transcript Quantification

Net-RSTQ

:: DESCRIPTION

Net-RSTQ is a software to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation.

::DEVELOPER

KUANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux
MatLab

:: DOWNLOAD

Net-RSTQ

:: MORE INFORMATION

Citation

Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.
Zhang W, Chang JW, Lin L, Minn K, Wu B, Chien J, Yong J, Zheng H, Kuang R.
PLoS Comput Biol. 2015 Dec 23;11(12):e1004465. doi: 10.1371/journal.pcbi.1004465.

SEL.TS.AREA v2 – Significance Analysis of Microarray Transcript Levels in Time Series Experiments

SEL.TS.AREA v2

:: DESCRIPTION

SEL.TS.AREA selects differentially expressed genes in time series experiments based on the area of the region bounded by the time series expression profiles to be compared, and considers the gene differentially expressed if the area exceeds a threshold based on a model of the experimental error.

::DEVELOPER

Barbara Di Camillo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/MacOsX/Linux
R package

:: DOWNLOAD

SEL.TS.AREA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S10.
Significance analysis of microarray transcript levels in time series experiments.
Di Camillo B, Toffolo G, Nair SK, Greenlund LJ, Cobelli C.

CorTo 1.03 – Transcript and Metabolite Network Reverse Engineering

CorTo 1.03

:: DESCRIPTION

CorTo is a tool for transcript and metabolite network reverse engineering. It combines several coexpression approaches and viewing capabilities, plus the possibility to detect over-representation of a particular functional class in a gene list.

::DEVELOPER

Usadel Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux
Java

:: DOWNLOAD

CorTo

:: MORE INFORMATION

RNA-eXpress 1.4.3 – Extract & Annotate Transcripts from Next Generation RNA sequencing data

RNA-eXpress 1.4.3

:: DESCRIPTION

RNA-eXpress was designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data. This approach complements existing gene annotation databases by ensuring all transcripts present in the sample are considered for further analysis.

::DEVELOPER

Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University

:: SCREENSHOTS

::REQUIREMENTS

Windows/Linux/MacOsX

:: DOWNLOAD

RNA-eXpress

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Mar 15;29(6):810-2. doi: 10.1093/bioinformatics/btt034. Epub 2013 Feb 8.
RNA-eXpress annotates novel transcript features in RNA-seq data.
Forster SC, Finkel AM, Gould JA, Hertzog PJ.

HALO 1.3 – Precise RNA de novo Transcript Half-life Determination

HALO 1.3

:: DESCRIPTION

HALO (Half-life Organizer) is the first software for the precise determination of transcript half-lives from measurements of RNA de novo transcription. In addition, methods for quality control, filtering and normalization are supplied. HALO provides a graphical user interface, command line tools and a well-documented Java API. Thus, it can be used both by biologists to determine transcript half-lives fast and reliably with the user interfaces provided as well as software developers integrating transcript half-life analysis into other gene expression profiling pipelines.

::DEVELOPER

Institut für Informatik, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

HALO

:: MORE INFORMATION

Citation

Caroline C. Friedel, Stefanie Kaufmann, Lars Dölken, Ralf Zimmer.
HALO – A Java framework for precise transcript half-life determination.
Bioinformatics, vol 26, no. 9, pp. 1264-1266, May 2010.