Annotare statistics

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Citations per year

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

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

This word cloud represents Annotare usage per disease context
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Protocols

Annotare specifications

Information


Unique identifier OMICS_00741
Name Annotare
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Publication for Annotare

Annotare citations

 (6)
library_books

The RNASeq er API—a gateway to systematically updated analysis of public RNA seq data

2017
Bioinformatics
PMCID: 5870697
PMID: 28369191
DOI: 10.1093/bioinformatics/btx143

[…] The analysis pipeline behind the RNASeq-er API offers an important service to researchers performing RNA-Seq experiments that choose to submit their data to ArrayExpress via https://www.ebi.ac.uk/fg/annotare submission tool: the deposited studies are not only described by rich, ontology-annotated experimental metadata; the associated raw data is also analysed for free, and for qualifying studies, […]

call_split

Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium

2017
eLife
PMCID: 5711377
PMID: 29110754
DOI: 10.7554/eLife.29132.031
call_split See protocol

[…] h) were performed by the University of Michigan DNA Sequencing Core using the Illumina Hi-Seq 2500 platform. All sequences were deposited in the EMBL-EBI ArrayExpress database (RRID:SCR_004473) using Annotare 2.0 and are cataloged under the accession number E-MTAB-5801. Transcriptional quantitation analysis was conducted using 64-bit Debian Linux stable version 7.10 ('Wheezy’). Pseudoalignment of […]

call_split

Identifying ultrasensitive HGF dose response functions in a 3D mammalian system for synthetic morphogenesis

2016
Sci Rep
PMCID: 5159920
PMID: 27982133
DOI: 10.1038/srep39178
call_split See protocol

[…] to SAM format using SAMTools v0.1.19.0. FPKM values were calculated from the mapped reads using Cufflinks v2.1.1. RNA-seq data (Raw and FPKM values) along with their FastQC files are available at the Annotare-ArrayExpress database (www.ebi.ac.uk/arrayexpress) under the accession number E-MTAB-4959. […]

call_split

Long Term and Transgenerational Effects of Stress Experienced during Different Life Phases in Chickens (Gallus gallus)

2016
PLoS One
PMCID: 4841578
PMID: 27105229
DOI: 10.1371/journal.pone.0153879
call_split See protocol

[…] beling and hybridization. In this way, we had one microarray with a pool of three individuals for each generation, sex and treatment group, altogether 48 birds. The microarray data can be accessed at Annotare (http://www.ebi.ac.uk/arrayexpress/) under accession E-MTAB-3623. […]

library_books

In vitro generation of human pluripotent stem cell derived lung organoids

2015
eLife
PMCID: 4370217
PMID: 25803487
DOI: 10.7554/eLife.05098.029

[…] derm (DE) was performed by the University of California, San Francisco DNA Sequencing Core using the Illumina Hi-Seq platform. All sequences were deposited in the EMBL-EBI ArrayExpress database using Annotare 2.0 and are catalogued under the accession number E-MTAB-3339 for the HLOs and E-MTAB-3158 for SC and DE. The University of Michigan Bioinformatics Core obtained the reads files and concatena […]

library_books

DNA Methylation and Transcription in a Distal Region Upstream from the Bovine AlphaS1 Casein Gene after Once or Twice Daily Milking

2014
PLoS One
PMCID: 4219721
PMID: 25369064
DOI: 10.1371/journal.pone.0111556

[…] s so that they could be annotated.The 39 bp reads thus generated were mapped on the Bos_taurus.UMD3.1.65 genome using IGV2.3 software from the Broad Institute. RNA-Seq data have been deposited on the Annotare website http://www.ebi.ac.uk/fg/annotare/; under accession number E-MTAB-2755. […]


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Annotare institution(s)
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA

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