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SARTools specifications

Information


Unique identifier OMICS_09104
Name SARTools
Alternative name Statistical Analysis of RNA-Seq data Tools
Software type Package/Module
Interface Command line 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
Stability Stable
Requirements
DESeq, edgeR, knitr, genefilter, xtable
Maintained Yes

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  • person_outline Hugo Varet <>

Publication for Statistical Analysis of RNA-Seq data Tools

SARTools in publications

 (8)
PMCID: 5896242
PMID: 29634949
DOI: 10.1016/j.ccell.2018.03.003

[…] sed to import the mapped counts data into r and summarize the transcripts-level data into gene level as described ((). counts for 21047 genes were normalized and further analyzed using deseq2 and the sartools packages (). differential gene expression was performed by fitting counts to a negative binomial generalized linear model using a multi-factorial design matrix (design formula of: regression  […]

PMCID: 5868158
PMID: 29616052
DOI: 10.3389/fpls.2018.00314

[…] with the default values (). reads per gene were counted using the htseq framework (). gene expression analysis was performed using r software (). bioconductor (), and deseq2 packages () from the sartools package (). normalization and differential analysis were carried out according to the deseq2 model (). the sequencing data are accessible in sra database under accession number prjna407426., […]

PMCID: 5839384
PMID: 29515753
DOI: 10.18632/oncotarget.23563

[…] after read count on gene features (featurecounts software, http://subread.sourceforge.net/), quantitative analysis of differential expression between conditions was performed by following the sartools pipeline (https://github.com/pf2-pasteur-fr/sartools) (see materials and methods for details)., gene expression data were normalized by a negative binomial distribution model by using deseq2 […]

PMCID: 5698469
PMID: 29162826
DOI: 10.1038/s41467-017-01832-6

[…] to each predicted cds was calculated for the 12 data sets by htseq-count with the -m union option. differential expression analysis (normalization and statistical tests) was performed using the sartools with deseq2 software and a bonferroni p-value adjustment was used to correct for multiple testing. genes with an adjusted p-value <0.05 were considered as differentially expressed. […]

PMCID: 5146858
PMID: 27931189
DOI: 10.1186/s12864-016-3367-x

[…] non coding rna validated by rfam and cds were counted with htseq-count [] using the abims roscoff platform. a list of differentially expressed genes was generated using an r software package: sartools [], embedded deseq2 [] and edger [] (modified t-test adjusted, pvalues < 0.05). a comparison of the results obtained with either deseq2 or edger produced a more exhaustive list using […]


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SARTools institution(s)
Institut Pasteur, Plate-forme Transcriptome & Epigenome, Biomics, Centre d’Innovation et Recherche Technologique (Citech), Paris, France; Institut Pasteur, Hub Bioinformatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP CNRS), Paris, France; CNRS, UPMC, ABiMS, Station Biologique, Roscoff, France
SARTools funding source(s)
This work was supported by the France Génomique National infrastructure, funded as part of the "Investissements d’Avenir" program managed by the Agence Nationale pour la Recherche (contract ANR-10-INBS-09).

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