Tag: Transcriptome

MR-JTI v1 – Joint-tissue Transcriptome-wide Association and Mendelian Randomization analysis

MR-JTI v1

:: DESCRIPTION

MR-JTI is a joint-tissue imputation (JTI) approach and a Mendelian randomization framework for causal inference.

::DEVELOPER

Gamazon Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R

:: DOWNLOAD

MR-JTI

 :: MORE INFORMATION

Citation

Zhou D, Jiang Y, Zhong X, Cox NJ, Liu C, Gamazon ER.
A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis.
Nat Genet. 2020 Nov;52(11):1239-1246. doi: 10.1038/s41588-020-0706-2. Epub 2020 Oct 5. PMID: 33020666; PMCID: PMC7606598.

TransPS 1.1.0 – Transcriptome Post Scaffolding

TransPS 1.1.0

:: DESCRIPTION

TransPS is a pipeline for post-processing of pre-assembled transcriptomes using reference based method.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 TransPS

:: MORE INFORMATION

Citation

A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs,
Computational Biology Journal, vol. 2014, Article ID 961823, 4 pages, 2014. doi:10.1155/2014/961823
Mingming Liu, Zach N. Adelman, Kevin M. Myles, and Liqing Zhang

Oases 0.2.09 – De novo Transcriptome Assembler for very short reads

Oases 0.2.09

:: DESCRIPTION

Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events, and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers.

::DEVELOPER

Daniel Zerbino

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Oases

:: MORE INFORMATION

Citation

Marcel H. Schulz, Daniel R. Zerbino, Martin Vingron and Ewan Birney
Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels
Bioinformatics (2012)doi: 10.1093/bioinformatics/bts094

TCW 3.2.5 – Transcriptome Computational Workbench

TCW 3.2.5

:: DESCRIPTION

TCW is a software package for assembling, annotating, querying, and comparing transcript and expression level data.

::DEVELOPER

Arizona Genomics Computational Lab (AGCoL)

:: SCREENSHOTS

TCW

:: REQUIREMENTS

  • Linux / MacOSX /Windows
  • Java

:: DOWNLOAD

 TCW

:: MORE INFORMATION

Citation:

PLoS One. 2013 Jul 17;8(7):e69401. doi: 10.1371/journal.pone.0069401. Print 2013.
TCW: transcriptome computational workbench.
Soderlund C1, Nelson W, Willer M, Gang DR.

MassBlast v0.9.13 – Accelarate Genome and Transcriptome data analysis

MassBlast v0.9.13

:: DESCRIPTION

MassBlast is a command line application to perform BLAST queries from multiple files against different databases at once.

::DEVELOPER

Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs/ Windows

:: DOWNLOAD

MassBlast

:: MORE INFORMATION

Citation

MassBlast: A workflow to accelerate RNA-seq and DNA database analysis
André Veríssimo, Jean-Etienne Bassard, Alice Julien-Laferrière, Marie-France Sagot, Susana Vinga
bioRxiv 131953; doi: https://doi.org/10.1101/131953

DeMixT 1.6.0 – Deconvolution on Transcriptome data from a mixture of two or three components

DeMixT 1.6.0

:: DESCRIPTION

DeMixT is a deconvolution framework for mixed transcriptomes from heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms.

::DEVELOPER

Statistical Bioinformatics Lab, The University of Texas M. D. Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • R package
  • BioCOnductor

:: DOWNLOAD

 DeMixT

:: MORE INFORMATION

Citation

Wang Z, Cao S, Morris JS, Ahn J, Liu R, Tyekucheva S, Gao F, Li B, Lu W, Tang X, Wistuba II, Bowden M, Mucci L, Loda M, Parmigiani G, Holmes CC, Wang W.
Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration.
iScience. 2018 Nov 30;9:451-460. doi: 10.1016/j.isci.2018.10.028. Epub 2018 Nov 2. PMID: 30469014; PMCID: PMC6249353.

Bioinformatics. 2013 Aug 1;29(15):1865-71. doi: 10.1093/bioinformatics/btt301.
DeMix: deconvolution for mixed cancer transcriptomes using raw measured data.
Ahn J, Yuan Y, Parmigiani G, Suraokar MB, Diao L, Wistuba II, Wang W.

Barnacle 1.0.4 – Detecting and Characterizing Tandem Duplications and Fusions in Transcriptome Assembly

Barnacle 1.0.4

:: DESCRIPTION

Barnacle (Browsing Assembled RNA for Chimeras with Localized Evidence) is a pipeline for detecting and characterizing chimeric transcripts from long RNA sequences, such as those generated by de novo transcriptome assembly.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Barnacle

:: MORE INFORMATION

Citation

BMC Genomics. 2013 Aug 14;14:550. doi: 10.1186/1471-2164-14-550.
Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies.
Swanson L et al.

HyLiTE 2.0.2 – Analyzes Transcriptome data from Allopolyploid Species

HyLiTE 2.0.2

:: DESCRIPTION

HyLiTE (Hybrid Lineage Transcriptome Explorer) analyzes transcriptome data from allopolyploid species. Allopolyploidy describes the formation of a new hybrid organism from the union of two or more different parents. Allopolyploid species carry multiple copies of each gene (homeologs), which often exhibit unusual expression patterns. Homeolog expression levels can be determined from next generation sequencing data (RNA-seq), but in practice, assigning reads to one homeolog over another is extremely challenging, particularly on a whole-genome scale. HyLiTE automates this process, and allows gene expression patterns to be explored even in very complex allopolyploid species.

::DEVELOPER

Professor Murray Cox, Massey University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ windows/MacOsX
  • Python

:: DOWNLOAD

 HyLiTE

:: MORE INFORMATION

Citation

W Duchemin, P-Y Dupont, MA Campbell, ARD Ganley and MP Cox. 2015.
HyLiTE: Accurate and Flexible Analysis of Gene Expression in Hybrid and Allopolyploid Species.
BMC Bioinformatics 16:8.

LongGF v0.1.2 – Detection of Gene Fusion by long-read Transcriptome Sequencing

LongGF v0.1.2

:: DESCRIPTION

LongGF is a fast computational tool to efficiently detect candidate gene fusion from long-read RNA-seq data, including cDNA sequencing data and direct mRNA sequencing data.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX / Windows
  • C++

:: DOWNLOAD

LongGF

:: MORE INFORMATION

Citation

Liu Q, Hu Y, Stucky A, Fang L, Zhong JF, Wang K.
LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing.
BMC Genomics. 2020 Dec 29;21(Suppl 11):793. doi: 10.1186/s12864-020-07207-4. PMID: 33372596; PMCID: PMC7771079.