Spanki 0.5.0 – Analysis of Alternative Splicing from RNA-Seq data

Spanki 0.5.0

:: DESCRIPTION

Spanki (Splicing Analysis Kit) is a set of tools to facilitate analysis of alternative splicing from RNA-Seq data. Spanki compiles quantitative and qualitative information about junction alignments from input BAM files, and analyzes junction-level splicing along with pairwise-defined splicing events. A simulator is also included to evaluate junction detection performance.

::DEVELOPER

The University of Maryland Center for Bioinformatics and Computational Biology (CBCB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • Python
  • BioPython

:: DOWNLOAD

 Spanki

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Nov 9;14:320. doi: 10.1186/1471-2105-14-320.
Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).
Sturgill D1, Malone JH, Sun X, Smith HE, Rabinow L, Samson ML, Oliver B.

SNPlice 1.8.0 – Find SNPs influencing splicing in NGS mRNA data

SNPlice 1.8.0

:: DESCRIPTION

SNPlice is a software tool to find and evaluate the co-occurrence of single-nucleotide-polymorphisms (SNP) and altered splicing in next-gen mRNA sequence reads.

::DEVELOPER

The Horvath Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 SNPlice

:: MORE INFORMATION

Citation

SNPlice: Variants that Modulate Intron-retention from RNA-sequencing Data.
Mudvari P, Movassagh M, Kowsari K, Seyfi A, Kokkinaki M, Edwards NJ, Golestaneh N, Horvath A.
Bioinformatics. 2014 Dec 6. pii: btu804

rSeqNP 1.0 – Detecting Differential Expression and Splicing from RNA-Seq data

rSeqNP 1.0

:: DESCRIPTION

rSeqNP is an R package using a non-parametric approach to test for differential expression (DE) and differential splicing (DS) of genes from RNA-seq data.

::DEVELOPER

Hui Jiang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 rSeqNP

:: MORE INFORMATION

Citation:

rSeqNP: A non-parametric approach for detecting differential expression and splicing from RNA-Seq data.
Shi Y, Chinnaiyan AM, Jiang H.
Bioinformatics. 2015 Feb 24. pii: btv119.

SplicingTypesAnno 1.0.2 – Annotation tool for alternative Splicing Types by RNA-Seq data

SplicingTypesAnno 1.0.2

:: DESCRIPTION

SplicingTypesAnno annotates four major splicing types by RNA-Seq data, including intron retention, exon skipping, alternative donor site, and alternative acceptor site. As a post-processing tool for alignment files, it annotates the alternative splicing types with details at the intron or exon level.

:: DEVELOPER

Dr. Xiaoyong Sun, Genomics and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows

:: DOWNLOAD

 SplicingTypesAnno

:: MORE INFORMATION

Citation

Comput Methods Programs Biomed. 2015 Feb 14. pii: S0169-2607(15)00028-0. doi: 10.1016/j.cmpb.2015.02.004. [Epub ahead of print]
SplicingTypesAnno: Annotating and quantifying alternative splicing events for RNA-Seq data.
Sun X, Zuo F, Ru Y, Guo J, Yan X, Sablok G

SPANR – Splicing-based Analysis of Variants

SPANR

:: DESCRIPTION

SPANR addresses a key unmet challenge in genomics research, which is to ascertain how single nucleotide variations (SNVs) cause splicing misregulation and may lead to disease. Unlike any other approach, this tool can analyze synonymous, missense and nonsense exonic SNVs, as well as intronic SNVs that are up to 300nt from splice junctions.

::DEVELOPER

the Frey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Hui Y. Xiong, et.al.
The human splicing code reveals new insights into the genetic determinants of disease.
Science DOI: 10.1126/science.1254806. Published Online December 18 2014.

rMATS 4.1.1 – replicate Multivariate Analysis of Transcript Splicing

rMATS 4.1.1

:: DESCRIPTION

rMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data.

::DEVELOPER

Xing Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python
  • Bowtie

:: DOWNLOAD

 rMATS

:: MORE INFORMATION

Citation

Shen S., Park JW., Lu ZX., Lin L., Henry MD., Wu YN., Zhou Q., Xing Y.
rMATS: Robust and Flexible Detection of Differential Alternative Splicing from Replicate RNA-Seq Data.
PNAS, 111(51):E5593-601. doi: 10.1073/pnas.1419161111

Shen S., Park JW., Huang J., Dittmar KA., Lu ZX., Zhou Q., Carstens RP., Xing Y.
MATS: A Bayesian Framework for Flexible Detection of Differential Alternative Splicing from RNA-Seq Data.
Nucleic Acids Research, 2012;40(8):e61 doi: 10.1093/nar/gkr1291

SpliceSeq 2.1 – Investigate alternative mRNA Splicing in Next Generation mRNA Sequence data

SpliceSeq 2.1

:: DESCRIPTION

SpliceSeq provides a quick, easy method of investigating alternative mRNA splicing in next generation mRNA sequence data. The tool may be used on a single mRNA-Seq sample to identify genes with multiple spliceforms or on a pair of samples to identify differential splicing between the samples. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 SpliceSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):2385-7. Epub 2012 Jul 20.
SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.
Ryan MC, Cleland J, Kim R, Wong WC, Weinstein JN.

nagnag 1.0.3 – Identifyng and Quantifying NAGNAG Alternative Splicing

nagnag 1.0.3

:: DESCRIPTION

nagnag is an R package for NAGNAG alternative splicing

:: DEVELOPER

Dr. Xiaoyong Sun, Genomics and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • R

:: DOWNLOAD

 nagnag

:: MORE INFORMATION

Citation

Biomed Res Int. 2014;2014:736798. doi: 10.1155/2014/736798. Epub 2014 Jun 5.
Computational evidence of NAGNAG alternative splicing in human large intergenic noncoding RNA.
Sun X, Lin SM, Yan X

nagnag: Identification and quantification of NAGNAG alternative splicing using RNA-Seq data.
Yan X, Sablok G, Feng G, Ma J, Zhao H, Sun X.
FEBS Lett. 2015 May 27. pii: S0014-5793(15)00423-8. doi: 10.1016/j.febslet.2015.05.029

ASGAL v1.1.6 – Alternative Splicing Graph ALigner

ASGAL v1.1.6

:: DESCRIPTION

ASGAL is a tool for detecting the alternative splicing events expressed in a RNA-Seq sample with respect to a gene annotation.

::DEVELOPER

AlgoLab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ASGAL

:: MORE INFORMATION

Citation

Denti L, Rizzi R, Beretta S, Vedova GD, Previtali M, Bonizzoni P.
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events.
BMC Bioinformatics. 2018 Nov 20;19(1):444. doi: 10.1186/s12859-018-2436-3. PMID: 30458725; PMCID: PMC6247705.

casper 2.26.0 – Characterization of Alternative Splicing based on Paired-End Reads

casper 2.26.0

:: DESCRIPTION

Casper is an R package for infering alternative splicing from paired-end RNA-seq data

::DEVELOPER

David Rossell <rosselldavid at gmail.com>, Camille Stephan-Otto, Manuel Kroiss, Miranda Stobbe, Victor Pena

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • R

:: DOWNLOAD

 Casper

:: MORE INFORMATION

Citation

Designing alternative splicing RNA-seq studies. Beyond generic guidelines.
Stephan-Otto Attolini C, Peña V, Rossell D.
Bioinformatics. 2015 Jul 27. pii: btv436