BioBin statistics

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Citations per year

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

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

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Popular tool citations

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Protocols

BioBin specifications

Information


Unique identifier OMICS_14120
Name BioBin
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A configuration file, LOKI database, a list of all individuals, phenotype file, region file, role file, weight file
Input format TXT, VCF
Output data Bins report, locus report
Operating system Unix/Linux, Mac OS
Programming languages C++
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.2.1
Stability Stable
Requirements
Boost, SQLite, Python, suds, apsw, liftOver binaries
Maintained Yes

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Documentation


Publications for BioBin

BioBin citations

 (9)
library_books

Rare variants in drug target genes contributing to complex diseases, phenome wide

2018
Sci Rep
PMCID: 5854600
PMID: 29545597
DOI: 10.1038/s41598-018-22834-4

[…] 797 DrugBank genes further used for association testing.For our association testing, we used a collapsing approach and binned all variants with minor allele frequency (MAF) <1% within the genes using Biobin. We also binned variants with MAF <1% using various filtering approaches described below:All Variants: All variants in the DrugBank genes (no filtering based on functionality)Functional annotat […]

library_books

Another Round of “Clue” to Uncover the Mystery of Complex Traits

2018
Genes
PMCID: 5852557
PMID: 29370075
DOI: 10.3390/genes9020061

[…] ciation of the contributions of multiple rare variants in collapsed regions on the phenotype of interest is the most popular method. Many analysis tools have been developed for these analyses such as BioBin [], Sequence Kernel Association Test (SKAT) [] , Variant Association Tools [], and RVTESTS []. Several genes containing rare variants have been identified with moderate to high effects on compl […]

library_books

PLATO software provides analytic framework for investigating complexity beyond genome wide association studies

2017
Nat Commun
PMCID: 5660079
PMID: 29079728
DOI: 10.1038/s41467-017-00802-2

[…] ioBin is open-source and available for download at http://www.ritchielab.com/software/biobin-download.BioBin is not built into PLATO and is essentially a pre-processing step where PLATO is concerned. BioBin, or other bioinformatics approaches, can be used to create the bins to pass into PLATO for a regression analysis. We will note that while PLATO will accept a VCF file as input for analysis, we […]

call_split

Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants

2017
Bioinformatics
PMCID: 5860358
PMID: 28968757
DOI: 10.1093/bioinformatics/btx559
call_split See protocol

[…] The framework of BioBin has been expanded to incorporate statistical methods, thereby enabling complete rare variant analysis, from binning to association testing, in one software. Burden and dispersion tests are two […]

library_books

Knowledge driven binning approach for rare variant association analysis: application to neuroimaging biomarkers in Alzheimer’s disease

2017
BMC Med Inform Decis Mak
PMCID: 5444041
PMID: 28539126
DOI: 10.1186/s12911-017-0454-0

[…] edge-driven binning approach (Bin-KAT) to identify trait- and disease-associated rare variants. Bin-KAT is a comprehensive, streamlined approach that unifies a genome-wide variant binning function in BioBin [–] and a dispersion-based association analysis tool such as SKAT [, ]. […]

call_split

Low Frequency Variants, Collapsed Based on Biological Knowledge, Uncover Complexity of Population Stratification in 1000 Genomes Project Data

2013
PLoS Genet
PMCID: 3873241
PMID: 24385916
DOI: 10.1371/journal.pgen.1003959
call_split See protocol

[…] BioBin is a standalone command line application written in C++ that uses a prebuilt LOKI database described below (software paper in preparation). Source distributions are available for Mac and Linux […]


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BioBin institution(s)
Duke University Medical Center, Duke General Surgery, Durham, NC, USA; Department of Biochemistry and Molecular Biology, Center for Systems Genomics, The Pennsylvania State University, PA, USA; Biomedical and Translational Informatics, Geisinger Health System, Danville, PA, USA
BioBin funding source(s)
This work was supported by NIH (grants LM010040, HL065962) and the Pennsylvania Department of Health Tobacco CURE Funds.

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