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RNASeqGUI specifications


Unique identifier OMICS_04029
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.1.0
Stability Stable
Maintained No


No version available

Publications for RNASeqGUI

RNASeqGUI citations


PIVOT: platform for interactive analysis and visualization of transcriptomics data

BMC Bioinformatics
PMCID: 5756333
PMID: 29304726
DOI: 10.1186/s12859-017-1994-0

[…] mplicated and time-consuming, but also breaks the integrity of the analysis workflow, limiting the sharing of global parameters, filtering criteria and analysis results between modules. Tools such as RNASeqGUI [], START [], ASAP [] and DEApp [] provide an interactive graphical interface for a small number of packages. But, these and other similar packages all adopt a rigid workflow design, have li […]


Glucose impairs tamoxifen responsiveness modulating connective tissue growth factor in breast cancer cells

PMCID: 5752499
PMID: 29312586
DOI: 10.18632/oncotarget.22552

[…] test method), normalization (upper quartile method), quantification of gene expression (SummerizeOverlaps option), and the analysis of differential expression (NoiSeq method) were carried out using “RNASeqGUI” []. A posterior probability threshold of 0.8 was used to select differentially expressed genes (DEGs). Pathway analysis was performed using PANTHER (Protein ANalysis THrough Evolutionary Re […]


Distinct Antigen Delivery Systems Induce Dendritic Cells’ Divergent Transcriptional Response: New Insights from a Comparative and Reproducible Computational Analysis

Int J Mol Sci
PMCID: 5372510
PMID: 28245601
DOI: 10.3390/ijms18030494
call_split See protocol

[…] Ensembl gene annotation (v67) using TopHat version 2.0.14 []. Only uniquely mapped reads were retained for further studies. Details can be found in . Analysis of aligned sequences was performed using RNASeqGUI [,]. RNASeqGUI automatically supports a fully reproducible data analysis. It automatically produces a dynamic report describing all the steps carried out during RNA-Seq data analysis and lin […]


Cripto is essential to capture mouse epiblast stem cell and human embryonic stem cell pluripotency

Nat Commun
PMCID: 5025790
PMID: 27586544
DOI: 10.1038/ncomms12589
call_split See protocol

[…] 500 platform (http://www.igatechnology.com/). Gene expression analysis was obtained by counting reads mapped on gene features, by using htseq-count and the statistical analysis was performed by using RNASeqGUI. In detail, paired-end fastq files were first aligned on the mouse genome version mm9 (downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/mm9/chromosomes) by using TopHat2 (version to […]


Computational Analysis of Single Nucleotide Polymorphisms Associated with Altered Drug Responsiveness in Type 2 Diabetes

Int J Mol Sci
PMCID: 4964384
PMID: 27347941
DOI: 10.3390/ijms17071008

[…] 3.3 workflow (Broad Institute, Cambridge, MA, USA) optimized for RNA-Seq reads, as described in []. Normalization, filtering, data inspection and general data analysis statistics were performed using RNASeqGUI []. […]


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RNASeqGUI institution(s)
Istituto per le Applicazioni del Calcolo, CNR, Napoli, Italy
RNASeqGUI funding source(s)
This work was supported by the Italian Flagship InterOmics Project (PB.P05), BMBS COST Action BM1006, PON01-02460.

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