SARTools statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SARTools
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Tool usage distribution map

This map represents all the scientific publications referring to SARTools per scientific context
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Associated diseases

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Protocols

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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Documentation


Maintainer


  • person_outline Hugo Varet

Publication for Statistical Analysis of RNA-Seq data Tools

SARTools citations

 (7)
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The Role of Programmed Cell Death Regulator LSD1 in Nematode Induced Syncytium Formation

2018
Front Plant Sci
PMCID: 5868158
PMID: 29616052
DOI: 10.3389/fpls.2018.00314
call_split See protocol

[…] ools 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.Ge […]

library_books

Effect of the diet type and temperature on the C. elegans transcriptome

2017
Oncotarget
PMCID: 5839384
PMID: 29515753
DOI: 10.18632/oncotarget.23563

[…] as R Bioconductor packages, perform read-count normalization by following a negative binomial distribution model. In order to automate this process and facilitate all group combination analysis, the SARTools pipeline [] was used. The resulting data was obtained as an .html file and .csv tables, including density count distribution analysis, pairwise scatter plots, cluster dendrograms, Principal C […]

library_books

Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria

2017
Nat Commun
PMCID: 5698469
PMID: 29162826
DOI: 10.1038/s41467-017-01832-6

[…] pping 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. RNA-seq da […]

library_books

The other white‐nose syndrome transcriptome: Tolerant and susceptible hosts respond differently to the pathogen Pseudogymnoascus destructans

2017
Ecol Evol
PMCID: 5606880
PMID: 28944007
DOI: 10.1002/ece3.3234

[…] osed sample groups using SARTools v.1.3.0 (Varet, Coppée, & Dillies, ), which streamlined the DESeq2 v.1.12.3 (Love, Huber, & Anders, ) and edgeR v3.14.0 (Robinson, McCarthy, & Smyth, ) analyses. The SARTools‐based DESeq2 settings included cooksCutoff = TRUE (perform outliers detection), independentFiltering = TRUE, alpha = 0.05 (threshold of statistical significance), pAdjustMethod = BH (benjamin […]

library_books

Adaptation of Propionibacterium freudenreichii to long term survival under gradual nutritional shortage

2016
BMC Genomics
PMCID: 5146858
PMID: 27931189
DOI: 10.1186/s12864-016-3367-x

[…] Finaly, 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 EdgeR. M […]

call_split

Expression and Regulation of PIWIL Proteins and PIWI Interacting RNAs in Rheumatoid Arthritis

2016
PLoS One
PMCID: 5125648
PMID: 27893851
DOI: 10.1371/journal.pone.0166920
call_split See protocol

[…] e [] and aligned to the piRNABank–database of 23`439 known human piRNA sequences.[] Reads Per Kilobase per Million mapped reads (RPKM) of piRNAs identified in RA were compared to RPKM in OA using the SARTools pipeline based on edgeR package.[] piRNAs were considered differentially expressed when the adjusted p-value was ≤ 0.05. […]


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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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