VAMP 2.2.8 – Visualisation and Analysis of CGH arrays, transcriptome and other Molecular Profiles

VAMP 2.2.8

:: DESCRIPTION

The VAMP software (Visualization and Analysis of array-CGH, transcriptome and other Molecular Profiles)allows the visual comparison of the array-CGH profiles of a cohort of patients, or the confrontation of array-CGH, expression and loss of heterozygosity profiles. VAMP offers many functionalities such as computing recurrent alterations, clustering profiles, crossing with clinical or biological annotations, performing syntenic projection onto the genome of another species.

::DEVELOPER

Bioinformatics Laboratory of Institut Curie (Paris).

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

VAMP

:: MORE INFORMATION

Citation:

Philippe La Rosa et al.
VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles
Bioinformatics 2006 22: 2066-2073;

RNA-Scoop v1.0.1 – Interactive Visualization of Single-cell Transcriptomes

RNA-Scoop v1.0.1

:: DESCRIPTION

RNA Scoop is a tool to visualize isoforms in single cell transcriptomes. Through use of an interactive cell cluster plot, users are able to explore isoforms in a single-cell transcriptome dataset of thousands of cells.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
JRE

:: DOWNLOAD

RNA Scoop

:: MORE INFORMATION

Citation

Stephenson M, Nip KM, HafezQorani S, Gagalova KK, Yang C, Warren RL, Birol I.
RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes.
NAR Genom Bioinform. 2021 Nov 29;3(4):lqab105. doi: 10.1093/nargab/lqab105. PMID: 34859209; PMCID: PMC8633890.

CStone – de novo Transcriptome Assembler

CStone

:: DESCRIPTION

CStone is a de novo assembler for RNA-Seq data that uses de Bruijn like graphs and annotates each contig produced with one of three graph classification levels indicating whether or not it can be guaranteed to be non chimeric.

::DEVELOPER

John Archer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
JRE

:: DOWNLOAD

CStone

:: MORE INFORMATION

Citation

Linheiro R, Archer J.
CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure.
PLoS Comput Biol. 2021 Nov 23;17(11):e1009631. doi: 10.1371/journal.pcbi.1009631. Epub ahead of print. PMID: 34813594.

TimesVector 1.5 – Analysis of Time Series Transcriptome data from multiple Phenotypes

TimesVector 1.5

:: DESCRIPTION

TimesVector is a triclustering tool for clustering time-series data that comprises multiple conditions, or phenotypes.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
R

:: DOWNLOAD

TimesVector

:: MORE INFORMATION

Citation

Jung I, Jo K, Kang H, Ahn H, Yu Y, Kim S.
TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes.
Bioinformatics. 2017 Dec 1;33(23):3827-3835. doi: 10.1093/bioinformatics/btw780. PMID: 28096084.

TERA-Seq – True end-to-end Sequencing of native RNA molecules for Transcriptome Characterization

TERA-Seq

:: DESCRIPTION

TERA-Seq (True End-to-end RNA Sequencing) is a platform that addresses these limitations, permitting more thorough transcriptome characterization.

::DEVELOPER

Z. MOURELATOS LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

TERA-Seq

:: MORE INFORMATION

Citation

Ibrahim F, Oppelt J, Maragkakis M, Mourelatos Z.
TERA-Seq: true end-to-end sequencing of native RNA molecules for transcriptome characterization.
Nucleic Acids Res. 2021 Aug 24:gkab713. doi: 10.1093/nar/gkab713. Epub ahead of print. PMID: 34428294.

Flux Capacitor 1.6.1 – Quantify Expressed Sequence Features from Transcriptome

Flux Capacitor 1.6.1

:: DESCRIPTION

The Flux Capacitor is a program to quantify expressed sequence features (e.g., genes or transcripts) from transcriptome interrogations by short read sequencing.

::DEVELOPER

Micha Sammeth

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Java

:: DOWNLOAD

Flux Capacitor

:: MORE INFORMATION

Citation

Nature. 2010 Apr 1;464(7289):773-7. doi: 10.1038/nature08903. Epub 2010 Mar 10.
Transcriptome genetics using second generation sequencing in a Caucasian population.
Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET.

miRDeep-P 1.3 / miRDP2 1.1.5 – Analyzing the microRNA Transcriptome in Plants

miRDeep-P 1.3 / miRDP2 1.1.5

:: DESCRIPTION

miRDeep-P (miRDP) is a tool which can be used to detecting miRNAs in plants from deeply sequenced small RNA libraries. It was developed by modifying miRDeep, which is based on a probabilistic model of miRNA biogenesis in animals, with a plant-specific scoring system and filtering criteria.

miRDP2 is adopted from miRDeep-P (miRDP) with new strategies and overhauled algorithm.

::DEVELOPER

Yang lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Perl

:: DOWNLOAD

miRDeep-P / miRDP2

:: MORE INFORMATION

Citation

Kuang Z, Wang Y, Li L, Yang X.
miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants.
Bioinformatics. 2019 Jul 15;35(14):2521-2522. doi: 10.1093/bioinformatics/bty972. PMID: 30521000.

Bioinformatics. 2011 Sep 15;27(18):2614-5. doi: 10.1093/bioinformatics/btr430. Epub 2011 Jul 19.
miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants.
Yang X1, Li L.

INTEGRATE 0.2.6 / INTEGRATE-Neo 1.2.1 – Gene Fusion Discovery using Whole Genome and Transcriptome data

INTEGRATE 0.2.6 / INTEGRATE-Neo 1.2.1

:: DESCRIPTION

INTEGRATE is a tool for calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data.

INTEGRATE-Neo is a tool for gene fusion neoantigen discovering tool using next-generation sequencing data.

::DEVELOPER

The Zhang Translational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

INTEGRATE / INTEGRATE-Neo

:: MORE INFORMATION

Citation

Zhang J, Mardis ER, Maher CA.
INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery.
Bioinformatics. 2017 Feb 15;33(4):555-557. doi: 10.1093/bioinformatics/btw674. PMID: 27797777; PMCID: PMC5408800.

Zhang J, White NM, Schmidt HK, Fulton RS, Tomlinson C, Warren WC, Wilson RK, Maher CA.
INTEGRATE: gene fusion discovery using whole genome and transcriptome data.
Genome Res. 2016 Jan;26(1):108-18. doi: 10.1101/gr.186114.114. Epub 2015 Nov 10. PMID: 26556708; PMCID: PMC4691743.

L_RNA_scaffolder – Long Transcriptome Reads to Scaffold Genome

L_RNA_scaffolder

:: DESCRIPTION

L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to scaffold genome fragments.

::DEVELOPER

L_RNA_scaffolder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler
Perl

:: DOWNLOAD

L_RNA_scaffolder

:: MORE INFORMATION

Citation:

BMC Genomics. 2013 Sep 8;14:604. doi: 10.1186/1471-2164-14-604.
L_RNA_scaffolder: scaffolding genomes with transcripts.
Xue W1, Li JT, Zhu YP, Hou GY, Kong XF, Kuang YY, Sun XW.

TranscriptSimulator 0.7 – Simulate Transcriptome Next-gen Reads, including 454 and Illumina

TranscriptSimulator 0.7

:: DESCRIPTION

TranscriptSimulator: Simple text-based, next-gen output simulator. Specifically designed to simulate transcriptome next-gen reads, including 454 and Illumina. Uses a model to simulate transcription followed by simulated sequencing using various customizable parameters. Uses a nucleotide gene set as a template (e.g. in silico predicted gene set). Version 0.70 has simulated SNPs/Indels with an improved model.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

TranscriptSimulator

:: MORE INFORMATION