Annotare statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Annotare

Tool usage distribution map

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

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Annotare specifications


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


No version available


Publication for Annotare

Annotare citations


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

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 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, […]


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

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 […]


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

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 ( under the accession number E-MTAB-4959. […]


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

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 ( under accession E-MTAB-3623. […]


In vitro generation of human pluripotent stem cell derived lung organoids

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 […]


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

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; 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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