Supersplat 1.0 – Spliced RNA-seq Alignment

Supersplat 1.0

:: DESCRIPTION

Supersplat is an appliction for discovery of potential splice junctions given HTS data.

::DEVELOPER

Mockler Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Supersplat

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Jun 15;26(12):1500-5. Epub 2010 Apr 21.
Supersplat–spliced RNA-seq alignment.
Bryant DW Jr, Shen R, Priest HD, Wong WK, Mockler TC.

 

RNASEQR 1.0.2 – Streamlined and Accurate RNA-seq Sequence Analysis program

RNASEQR 1.0.2

:: DESCRIPTION

RNASEQR is a nucleotide sequence mapper/aligner and is designed specifically for RNA-seq data analysis. It takes advantage of annotated transcripts and genomic reference sequences to obtain high quality mapping/alignment results.

::DEVELOPER

Hood Lab at ISB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  RNASEQR

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Mar;40(6):e42. Epub 2011 Dec 22.
RNASEQR–a streamlined and accurate RNA-seq sequence analysis program.
Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE.

ERANGE 4.0a – Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq

ERANGE 4.0a

:: DESCRIPTION

The functions of ERANGE are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (‘multireads’), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candida

::DEVELOPER

the Wold Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ERANGE

:: MORE INFORMATION

Citation

Nat Methods. 2008 Jul;5(7):621-8. Epub 2008 May 30.
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B.

 

ShortFuse 0.2 – Gene Fusion Detection using Ambiguously Mapping RNA-Seq Read Pairs

ShortFuse 0.2

:: DESCRIPTION

ShortFuse is a software to identify fusions with ambiguously mapping read pairs without generating numerous spurious fusions from the many mapping locations.

::DEVELOPER

Marcus Kinsella

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ShortFuse

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 15;27(8):1068-75. Epub 2011 Feb 16.
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V.

RSEQtools 0.6 – Analyze RNA-Seq data using Compact and Anonymized data summaries

RSEQtools 0.6

:: DESCRIPTION

RSEQtools is a suite of tools that use Mapped Read Format (MRF) for the analysis of RNA-Seq experiments. MRF was developed to address privacy concerns associated with the potential for mRNA sequence reads to identify and genetically characterise specific individuals; it is a compact data summary format that enables anonymization of confidential sequence information, while maintaining the ability to conduct subsequent functional genomics studies. RSEQtools provides a suite of modules that convert to/from MRF data and perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads, and segmenting that signal into actively transcribed regions.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RSEQtools

:: MORE INFORMATION

Citation:

Lukas Habegger*, Andrea Sboner*, Tara A. Gianoulis, Joel Rozowsky, Ashish Agarwal, Michael Snyder, Mark Gerstein.
RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonymized data summaries.
Bioinformatics (2011) 27 (2): 281-283.

IQSeq 1.0 – Isoform Quantification with RNA-seq data

IQSeq 1.0

:: DESCRIPTION

IQSeq is a tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use an EM algorithm to infer the most probable expression level for each isoform of a gene.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 IQSeq

:: MORE INFORMATION

Citation:

Jiang Du, Jing Leng, Lukas Habegger, Andrea Sboner, Drew McDermott, Mark Gerstein.
IQSeq: Integrated Isoform Quantification Analysis Based on Next-generation Sequencing
PLoS ONE 7(1): e29175. doi:10.1371/journal.pone.0029175

RD – Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation

RD

:: DESCRIPTION

RD is intended to implement a program for statistical estimation of isoform expression levels using RNA-Seq based on the modeling of RNA degradation.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RD

:: MORE INFORMATION

Citation

Wan L, Yan XT, Chen T and Sun FZ (2011)
RD: A Program for Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation
submitted.

CEDER – Detection of Differentially Expressed Genes by combining significance of exons using RNA-Seq

CEDER

:: DESCRIPTION

CEDER is intended to implement a program for detecting differentially expressed genes (DEG) using RNA-Seq by combining significance of exons within a gene.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CEDER

:: MORE INFORMATION

Citation

Wan L, Sun FZ (2011):
CEDER: Accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq
(submitted to APBC2012).

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