BioBin protocols

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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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Publication for BioBin

BioBin in pipeline

2009
PMCID: 2795765
PMID: 19954539
DOI: 10.1186/1471-2180-9-248

[…] generated by the bioedit sequence alignment editor (version 7.0.1) []. nucleotide sequences were translated using translate nucleic acid sequences software []http://biotools.umassmed.edu/cgi-bin/biobin/transeq. neighbor-joining phylogenetic tree topologies of nucleotide and predicted amino acid alignments were constructed using the mega (molecular evolutionary genetics analysis) 3.1 software […]

BioBin in publications

 (6)
PMCID: 5854600
PMID: 29545597
DOI: 10.1038/s41598-018-22834-4

[…] genes further used for association testing.table 4, 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 […]

PMCID: 5852557
PMID: 29370075
DOI: 10.3390/genes9020061

[…] 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 […]

PMCID: 3873241
PMID: 24385916
DOI: 10.1371/journal.pgen.1003959

[…] have been shown to be much more powerful than single-variant association testing for low frequency variants –, and thus are reliable to detect population stratification. our collapsing method, biobin, provides the opportunity to cast a broader net and uncover stratification across meaningful elements such as genes, pathways, and evolutionary conserved regions by aggregating low frequency […]

PMCID: 3781043
PMID: 24086489
DOI: 10.1371/journal.pone.0075268

[…] and g. raimondii). to identify sequences containing a udp-binding consensus sequences, all probe sets were translated into the 6 possible reading frames (http://biotools.umassmed.edu/cgi-bin/biobin/transeq), then subjected to a motif search using geneious pro software program [] with the expasy prosite accession #ps00375 for the pspg motif [,]., two probe sets from affymetrix microarray, […]

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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