ImmuneDB statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ImmuneDB
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ImmuneDB specifications

Information


Unique identifier OMICS_12746
Name ImmuneDB
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data Some IGHV sequences, optionally pre-processed by pRESTO.
Input format FASTA,FASTQ
Output data Some raw sequences, metadata, mutation analysis, and clonal assignments.
Output format FASTA,FASTQ,CSV
Operating system Unix/Linux
Programming languages Python
Database management system MySQL
Computer skills Advanced
Version 0.25.1
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Uri Hershberg

Additional information


A free trial is available on the site.

Publication for ImmuneDB

ImmuneDB citations

 (4)
library_books

Next Generation Sequencing of Antibody Display Repertoires

2018
Front Immunol
PMCID: 5810246
PMID: 29472918
DOI: 10.3389/fimmu.2018.00118

[…] r clustering unique sequences (). VDJFasta uses an HMM to accurately predict all VH and VL CDRs, as well as the GS linker sequence for scFv fragments, and can generate library diversity plots (). The ImmuneDB package aligns sequences based on a query sequence, such as a framework region, to delineate CDR regions (). ImmuneDB also performs mutational and statistical analysis on the sequence library […]

library_books

System analysis of the regulation of the immune response by CD147 and FOXC1 in cancer cell lines

2018
Oncotarget
PMCID: 5849184
PMID: 29560120
DOI: 10.18632/oncotarget.24161

[…] genes (Immu_Genes) derived from the intersection of genes from InnateDB database (http://www.innatedb.com) [] and Immunogenetic Related Information Source database (IRIS) (http://jtpc4.path.cam.ac.uk/immunedb/IRIS/home.htm) []. Next, we intersected the 662 genes with the list of genes in the CCLE. Finally, we obtained 627 Immu_Genes for further analysis. We found that the level of Immu_Genes mRNA […]

library_books

Integrative gene network analysis identifies key signatures, intrinsic networks and host factors for influenza virus A infections

2017
NPJ Syst Biol Appl
PMCID: 5712526
PMID: 29214055
DOI: 10.1038/s41540-017-0036-x

[…] icantly enriched in DOCK5-CCGS(7) (FET p = 3.6e-5, 1.2-fold), SRGs(7) (FET p = 1.2e−8, 1.4-fold) and JTGsdown(7) (FET p = 5.4e−7, 1.4-fold) (Table ). The innate immune system-related genes curated by ImmuneDB are significantly enriched in DOCK5-CCGS(7) (FET p = 9.3e−10, 1.4-fold), SRGs (FET p = 5.6e−12, 1.7-fold), JTGsup(7) (FET p = 2.7e−15, 2.6-fold), but not in JTGdown(7), indicating the typical […]

library_books

ED SUMM: B cell VH region repertoire sequencing of 8 anatomical sites in 6 human donors reveals distinct networks of clone distribution

2017
Nat Biotechnol
PMCID: 5679700
PMID: 28829438
DOI: 10.1038/nbt.3942

[…] via SRA under accession number PRJNA343738. Analyzed data (VDJ assignment, clonal lineage assignment, somatic hypermutation selection analysis etc.) are available for viewing and download at (http://immunedb.com/tissue-atlas). A description of the immune database that was constructed for viewing these data is provided in http://immunedb.com . Listings of C20 clones in the two most highly sequence […]


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ImmuneDB institution(s)
School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA
ImmuneDB funding source(s)
This work was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Award Number P01AI106697 and by NIH P30-CA016520.

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