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.

Traph 0.7.2 – Transcript Identification and Quantification with RNA-Seq

Traph 0.7.2

:: DESCRIPTION

Traph (Transcripts in gRAPHs) is a software for RNA transcript expression prediction from RNA-sequencing data.

::DEVELOPER

GSA (Genome-scale algorithmics) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Traph

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 5:S15. doi: 10.1186/1471-2105-14-S5-S15. Epub 2013 Apr 10.
A novel min-cost flow method for estimating transcript expression with RNA-Seq.
Tomescu AI, Kuosmanen A, Rizzi R, M?kinen V.

Cufflinks 2.2.1 – Transcript Assembler & Abundance Estimator for RNA-Seq

Cufflinks 2.2.1

:: DESCRIPTION

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

::DEVELOPER

Cole Trapnell’s lab at the University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

Cufflinks

:: MORE INFORMATION

Citation

Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L.
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Nature Biotechnology doi:10.1038/nbt.1621

piClust – Find piRNA Clusters and Transcripts from small RNA-seq data

piClust

:: DESCRIPTION

piClust uses a density based clustering approach without assumption of any parametric distribution to improve piRNA cluster identification.

::DEVELOPER

B&H Lab, Sun Kim group, Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

piClust: a density based piRNA clustering algorithm.
Jung I, Park JC, Kim S.
Comput Biol Chem. 2014 Jun;50:60-7. doi: 10.1016/j.compbiolchem.2014.01.008.

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

EMSAR v2.0.1 – Quantify Transcripts from RNA-seq data

EMSAR v2.0.1

:: DESCRIPTION

EMSAR (Estimation by Mappability-based Segmentation And Reclustering) is a new approach for quantifying transcript abundance from RNA-seq data.The software groups reads according to the set of transcripts to which they are mapped and finds maximum likelihood estimates using a joint Poisson model for each optimal set of segments of transcripts.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  EMSAR

:: MORE INFORMATION

Citation

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.
Lee S, Seo CH, Alver BH, Lee S, Park PJ.
BMC Bioinformatics. 2015 Sep 3;16(1):278. doi: 10.1186/s12859-015-0704-z.

PPIXpress 1.23 – Specific Protein Interaction Networks from Transcript Expression

PPIXpress 1.23

:: DESCRIPTION

PPIXpress exploits expression data at the transcript-level and is thus able to also reveal alterations in protein connectivity caused by alternative splicing.

::DEVELOPER

PPIXpress team

:: SCREENSHOTS

PPIXpress

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 PPIXpress

:: MORE INFORMATION

Citation

PPIXpress: construction of condition-specific protein interaction networks based on transcript expression.
Will T, Helms V.
Bioinformatics. 2015 Oct 27. pii: btv620.

MiTie 1.0.0 – Simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples

MiTie 1.0.0

:: DESCRIPTION

MITIE (Mixed Integer Transcript IdEntification) is a software for simultaneous transcript reconstruction and quantification.

::DEVELOPER

the Biomedical Informatics Lab of Prof. Dr. Gunnar Rätsch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MiTie

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Oct 15;29(20):2529-2538.
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.
Behr J, Kahles A, Zhong Y, Sreedharan VT, Drewe P, Rätsch G.

IsoSCM 2.0.12 – Transcript Assembly tool using Multiple Change-point Inference to improve 3’UTR Annotation

IsoSCM 2.0.12

:: DESCRIPTION

IsoSCM (Isoform Structural Change Model) is a new method for transcript assembly  that incorporates change-point analysis to improve the 3′ UTR annotation process.

::DEVELOPER

IsoSCM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows
  • Java

:: DOWNLOAD

  IsoSCM

:: MORE INFORMATION

Citation

RNA. 2015 Jan;21(1):14-27. doi: 10.1261/rna.046037.114. Epub 2014 Nov 18.
IsoSCM: improved and alternative 3′ UTR annotation using multiple change-point inference.
Shenker S, Miura P, Sanfilippo P, Lai EC

HISAT / HISAT2 2.1.0 – Hierarchical Indexing for Spliced Alignment of Transcripts

HISAT / HISAT2 2.1.0

:: DESCRIPTION

HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads.

HISAT2 is a successor to both HISAT and TopHat2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 HISAT2

:: MORE INFORMATION

Citation

HISAT: a fast spliced aligner with low memory requirements.
Kim D, Langmead B, Salzberg SL.
Nat Methods. 2015 Apr;12(4):357-60. doi: 10.1038/nmeth.3317.