TeXP v1.0 – Quantifying Abundances of Transposable Elements transcripts from RNA-Seq data

TeXP v1.0

:: DESCRIPTION

TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

TeXP

:: MORE INFORMATION

Citation:

PLoS Comput Biol. 2019 Aug 19;15(8):e1007293. doi: 10.1371/journal.pcbi.1007293. eCollection 2019 Aug.
TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements.
Navarro FC, Hoops J, Bellfy L, Cerveira E, Zhu Q, Zhang C, Lee C, Gerstein MB

ALoFT 1.0 – Annotation of Loss-of-Function Transcripts

ALoFT 1.0

:: DESCRIPTION

ALoFT provides extensive annotations to putative loss-of-function variants (LoF) in protein-coding genes including functional, evolutionary and network features. Further, ALoFT can predict the impact of premature stop variants and classify them as dominant disease-causing, recessive disease-causing and benign variants.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ALoFT

:: MORE INFORMATION

Citation:

Nat Commun. 2017 Aug 29;8(1):382. doi: 10.1038/s41467-017-00443-5.
Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes.
Balasubramanian S, Fu Y, Pawashe M, McGillivray P, Jin M, Liu J, Karczewski KJ, MacArthur DG, Gerstein M

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.