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This map represents all the scientific publications referring to Eoulsan per scientific context
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chevron_left Spliced read alignment Read alignment Differential expression Read quality control Libraries/frameworks Normalization File format conversion PaaS Bioinformatics workflows Transcriptome annotation chevron_right
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Protocols

Eoulsan specifications

Information


Unique identifier OMICS_01402
Name Eoulsan
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Parallelization MapReduce
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes

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Publication for Eoulsan

Eoulsan citations

 (11)
library_books

Connexin 43 Controls the Astrocyte Immunoregulatory Phenotype

2018
Brain Sci
PMCID: 5924386
PMID: 29565275
DOI: 10.3390/brainsci8040050

[…] 0 device (Illumina, San Diego, CA, USA). A mean of 50 ± 18 million passing Illumina quality filter reads was obtained for each sample.RNASeq bioinformatics analysis: Analyses were performed using the Eoulsan pipeline version 2.0-alpha5 [], including read filtering, mapping, alignment filtering, read quantification. Before mapping, reads ≤40 bases were removed, and reads with quality mean ≤30 were […]

call_split

Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms

2018
Sci Rep
PMCID: 5859163
PMID: 29556065
DOI: 10.1038/s41598-018-23106-x
call_split See protocol

[…] E) models by adapting the methodology applied in and. Estimation of expression (normalized DESeq counts) and differential gene expression analysis at different stages of the study was performed using Eoulsan, using parameters as indicated in Eoulsan parameter file used, (File S3). Statistical analysis to compare the expression of genes was performed using two-sample t-test with unequal variance. […]

call_split

Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction

2017
Biotechnol Biofuels
PMCID: 5588705
PMID: 28912831
DOI: 10.1186/s13068-017-0897-7
call_split See protocol

[…] bp paired-end read sequencing on a HiSeq 1500 device. A mean of 52 ± 10 million passing Illumina quality filter reads was obtained for each of all the samples. We performed RNA-seq analysis using the Eoulsan pipeline []. Only read 1 was considered for the further analyses. Before mapping, poly N read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 were discarded. […]

call_split

Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis acting elements

2017
PLoS Genet
PMCID: 5549768
PMID: 28749941
DOI: 10.1371/journal.pgen.1006903
call_split See protocol

[…] llumina HiSeq system (E9.5 embryos) or using 42 bp paired-end reads on an Illumina NextSeq (E8.5 embryos) according to the manufacturer’s specifications. Chip-seq data were analysed as follows, using Eoulsan [] with extended support for ChIP-seq workflows (https://github.com/GenomicParisCentre/eoulsan/tree/branch-chip-seq). First, reads were filtered out when they would not pass Illumina filters ( […]

call_split

Translation in astrocyte distal processes sets molecular heterogeneity at the gliovascular interface

2017
PMCID: 5368712
PMID: 28377822
DOI: 10.1038/celldisc.2017.5
call_split See protocol

[…] Analyses were performed using the Eoulsan pipeline [], including read filtering, mapping, alignment filtering, read quantification. Before mapping, reads ⩽40 bases were removed, and reads with quality mean ⩽30 were discarded. Reads we […]

call_split

A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness

2016
Biotechnol Biofuels
PMCID: 4812632
PMID: 27030800
DOI: 10.1186/s13068-016-0488-z
call_split See protocol

[…] scripts that exhibited an SD >20 % of the mean value within replicates, false discovery rates ([] were used to assess the significance of values. Data from RNA deep sequencing were analysed using the EOULSAN software version 1.2.2 []. To quantify the gene expression level, the relative transcript abundance was measured in reads per kb of exon per million mapped sequence reads (RPKM; []). All trans […]


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Eoulsan institution(s)
École normale supérieure, Institut de Biologie de l’ENS, IBENS, Paris, France; Inserm, U1024, Paris, France; CNRS, UMR 8197, Paris, France; Plate-forme Transcriptome et Epigénome, Institut Pasteur, Paris, France
Eoulsan funding source(s)
Supported by the network Infrastructures en Biologie Santé et Agronomie (IBiSA) and by an Amazon Web Services research grant.

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