CTCM – Classifying Transcripts from Coral Metatranscriptome

CTCM

:: DESCRIPTION

CTCM classifies the transcripts assembled from coral metatranscriptome for coral and symbiodinium based on alignments. CTCM is evaluated by simulated datasets and real datasets, it can genereate more sensitive and specific classification for coral and symbiodinium than existed methods.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

CTCM

:: MORE INFORMATION

TAG 0.91 – Transcript Assembly by Mapping Reads to Graphs

TAG 0.91

:: DESCRIPTION

TAG is a tool for metatranscriptome assembly using de Bruijn graph of matched metagenome as the reference

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TAG

:: MORE INFORMATION

Citation:

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis.
Ye Y, Tang H.
Bioinformatics. 2015 Aug 29. pii: btv510.

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.

BitSeq 0.7.5 / for R 1.16.0 – Bayesian Inference of Transcripts from Sequencing Data

BitSeq 0.7.5 / for R 1.16.0

:: DESCRIPTION

BitSeq is an application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. An advantage of this approach is the ability to account for both technical uncertainty and intrinsic biological variance in order to avoid false DE calls. The technical contribution to the uncertainty comes both from finite read-depth and the possibly ambiguous mapping of reads to multiple transcripts.

:: DEVELOPER

Peter Glaus , Antti Honkela

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • GCC / BioCOnductor/ R package
  • Python

:: DOWNLOAD

 BitSeq / for R

:: MORE INFORMATION

Citation

Fast and accurate approximate inference of transcript expression from RNA-seq data.
Hensman J, Papastamoulis P, Glaus P, Honkela A, Rattray M.
Bioinformatics. 2015 Aug 26. pii: btv483

Bioinformatics. 2012 Jul 1;28(13):1721-8. doi: 10.1093/bioinformatics/bts260. Epub 2012 May 3.
Identifying differentially expressed transcripts from RNA-seq data with biological variation.
Glaus P, Honkela A, Rattray M.

HISAT / HISAT2 2.0.3-beta – Hierarchical Indexing for Spliced Alignment of Transcripts

HISAT / HISAT2 2.0.3-beta

:: 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.

IsoSCM 2.0.11 – Transcript Assembly tool using Multiple Change-point Inference to improve 3’UTR Annotation

IsoSCM 2.0.11

:: 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

GRIT 1.1.3 – Genome-guided Transcript Assembly Tool

GRIT 1.1.3

:: DESCRIPTION

GRIT (Generalized RNA Integration Tool) is a tool for transcript discovery and quantification via the integrated analysis of CAGE, RAMPAGE, RNAseq, and poly(A)-seq data

::DEVELOPER

Nathan Boley  ( nboley (AT) berkeley.edu ) in collaboration with the Bickel and Celniker groups.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GRIT

:: MORE INFORMATION

Citation

Nat Biotechnol. 2014 Apr;32(4):341-6. doi: 10.1038/nbt.2850. Epub 2014 Mar 16.
Genome-guided transcript assembly by integrative analysis of RNA sequence data.
Boley N, Stoiber MH, Booth BW, Wan KH, Hoskins RA, Bickel PJ, Celniker SE, Brown JB

PPIXpress 1.05 – Specific Protein Interaction Networks from Transcript Expression

PPIXpress 1.05

:: 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

Thorsten Will  , Volkhard Helms

:: 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.

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.

AS-EAST 1.1.1 – Annotate and Analyzes users’ uploaded Transcript data

AS-EAST 1.1.1

:: DESCRIPTION

AS-EAST (Alternative Splicing Effects ASsessment Tools) is an online tool for the functional annotation of putative proteins encoded by transcripts generated by alternative splicing (AS).

::DEVELOPER

Nagahama Institute of Bio-Science and Technology

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 1;28(15):2076-7. doi: 10.1093/bioinformatics/bts320.
AS-EAST: a functional annotation tool for putative proteins encoded by alternatively spliced transcripts.
Shionyu M, Takahashi K, Go M.