ImmuneDB statistics

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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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Documentation


Maintainer


  • person_outline Uri Hershberg <>

Additional information


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Publication for ImmuneDB

ImmuneDB in publications

 (3)
PMCID: 5810246
PMID: 29472918
DOI: 10.3389/fimmu.2018.00118

[…] 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 […]

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

[…] (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 […]

PMCID: 5712526
PMID: 29214055
DOI: 10.1038/s41540-017-0036-x

[…] 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 […]


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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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