Nebula statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool Nebula
info

Tool usage distribution map

This map represents all the scientific publications referring to Nebula per scientific context
info info

Associated diseases

info

Popular tool citations

chevron_left Read alignment Bioinformatics workflows De novo motif discovery Peak calling Peak annotation chevron_right
Want to access the full stats & trends on this tool?

Nebula specifications

Information


Unique identifier OMICS_00424
Name Nebula
Interface Web user interface
Restrictions to use None
Programming languages Perl, R
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Publication for Nebula

Nebula citations

 (6)
library_books

Id Proteins Suppress E2A Driven Invariant Natural Killer T Cell Development prior to TCR Selection

2018
Front Immunol
PMCID: 5787561
PMID: 29416542
DOI: 10.3389/fimmu.2018.00042

[…] n 1.1.2, parameters: -chunkmbs 128 -mm -m1 -best -strata -p4 -S -q). Peaks were called using MACS () (version 1.4.2, default parameters). Peaks were then annotated by the NGS: Peak Annotation tool on Nebula (). Bed and wiggle files were generated by MACS for visualization using the Integrative Genomic Viewer (). De novo motif analysis was done using the findmotifs.pl program with HOMER () (v4.7.2, […]

library_books

IRF8 dependent molecular complexes control the Th9 transcriptional program

2017
Nat Commun
PMCID: 5727025
PMID: 29233972
DOI: 10.1038/s41467-017-01070-w

[…] sequenced with paired-end 75 bp reads. Sequenced reads were aligned to the mouse genome (mm10 assembly) with Bowtie 3. The output of Bowtie was converted to BED files using MACS (Version 1.0.1). The Nebula-web server was then used for peak calling with FindPeaks, de novo motif discovery with ChIPMunk and statistical analysis. The Golden Helix genome browser software allowed us to visualise the pe […]

library_books

Robust diagnosis of Ewing sarcoma by immunohistochemical detection of super enhancer driven EWSR1 ETS targets

2017
Oncotarget
PMCID: 5788584
PMID: 29416716
DOI: 10.18632/oncotarget.20098

[…] Publicly available data were retrieved from the Gene Expression Omnibus (GEO). ENCODE SK-N-MC DNase-Seq (GSM736570) [] were analyzed in the Nebula environment [] using Model-based Analysis of ChIP-Seq v1.4.2 (MACS) [] and converted to *.wig format for display in the UCSC Genome Browser []. Preprocessed ChIP-Seq data from Riggi et al. [] ( […]

library_books

Lysosome associated membrane glycoprotein 1 predicts fratricide amongst T cell receptor transgenic CD8+ T cells directed against tumor associated antigens

2016
Oncotarget
PMCID: 5302936
PMID: 27447745
DOI: 10.18632/oncotarget.10647

[…] Publicly available DNase-seq and ChIP-seq data was performed as previously described []. Briefly, data were retrieved from the GEO. ENCODE [] SK-N-MC DNase-seq (GSM736570) were analysed within the Nebula environment [] using Model-based Analysis of ChIP-Seq v1.4.2 (MACS) [] and converted to *. wig format for display in the UCSC Genome Browser []. Pre-processed ChIP-seq data from Riggi et al. (G […]

library_books

Genome wide Twist1 occupancy in endocardial cushion cells, embryonic limb buds, and peripheral nerve sheath tumor cells

2014
BMC Genomics
PMCID: 4190347
PMID: 25262113
DOI: 10.1186/1471-2164-15-821

[…] with genes that are expressed in each cell type were then compared with each other to identify peaks shared between datasets (ECC-Limb, ECC-PNST, Limb-PNST, and ECC-Limb-PNST) using IntersectBed from Nebula with a minimum overlap of 5% of the nucleotides in shared peaks []. Genomic sequences for each of the binding peak sequences (~50 bp to 750 bp in length) were obtained using Genomatix Software […]

library_books

The DEK oncoprotein binds to highly and ubiquitously expressed genes with a dual role in their transcriptional regulation

2014
Mol Cancer
PMCID: 4175287
PMID: 25216995
DOI: 10.1186/1476-4598-13-215

[…] The “Genomic annotation of ChIP-seq peaks” tool in the Nebula software package [] was used with default parameters to find the closest gene to each DEK peak and calculate the distance from the transcription start site to the middle of the peak. The same t […]


Want to access the full list of citations?
Nebula institution(s)
Institut Curie, Paris, France; INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris, France; Mines ParisTech, Fontainebleau, France; INSERM, U830, Genetics and Biology of Cancers, Paris, France
Nebula funding source(s)
Supported by The ‘Projet Incitatif et Collaboratif Bioinformatique et Biostatistiques’ of the Institut Curie, and the Ligue Nationale Contre le Cancer.

Nebula reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Nebula