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Biofilter specifications

Information


Unique identifier OMICS_17679
Name Biofilter
Software type Package/Module
Interface Command line interface
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Database management system SQLite
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.4.1
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Additional information


https://ritchielab.psu.edu/research/research-areas/expert-knowledge-bioinformatics/methods/biofilter

Publications for Biofilter

Biofilter citations

 (22)
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

[…] unique list of 829 genes and 957 drugs after removing duplicates.We also retrieved chromosome and base pair locations for these 829 unique DrugBank genes in the latest genome assembly build 38 using Biofilter version 2.4 and the (Library of Knowledge Integration) LOKI database version 2.2. Of the list of 829 genes, 19 gene identifiers, listed in Supplementary Table , were unrecognized by the Biof […]

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

[…] ect p value cutoff of 0.01 from the main effect analysis described previously, which left us with 256 SNPs. PLATO automatically performed pairwise interactions between every combination of these SNPs.Biofilter software was employed as an automated knowledge-driven filter, using the data across many biological databases. Biofilter accesses several publicly available biological knowledge databases t […]

call_split

Discovery and replication of SNP SNP interactions for quantitative lipid traits in over 60,000 individuals

2017
BioData Min
PMCID: 5525436
PMID: 28770004
DOI: 10.1186/s13040-017-0145-5
call_split See protocol

[…] TC (n = 16,849), and TG (n = 13,031).Fig. 1 Additional quality control metrics were applied to the individual lipid datasets for each of the statistical analyses. For both the main effect filter and Biofilter analyses, SNPs with missing phenotypes were removed along with variants with minor allele frequency (MAF) < 0.05 or missing genotype rate > 5%. For the main effect filter analysis, SNPs were […]

library_books

Incorporation of Biological Knowledge Into the Study of Gene Environment Interactions

2017
Am J Epidemiol
PMCID: 5860556
PMID: 28978191
DOI: 10.1093/aje/kwx229

[…] ion data pointed to the same biological pathway that might interact with smoking in modifying cancer risk.To integrate this type of biological knowledge into an analysis, bioinformatics tools such as Biofilter can be used. Biofilter is a knowledge integration tool developed to allow for annotation, filtering, and model building of genomic data (, ). The underlying database of biological knowledge […]

library_books

The Integration of Epistasis Network and Functional Interactions in a GWAS Implicates RXR Pathway Genes in the Immune Response to Smallpox Vaccine

2016
PLoS One
PMCID: 4981436
PMID: 27513748
DOI: 10.1371/journal.pone.0158016

[…] gene network approach, Franke et al. [] demonstrated that genes for multigenic disorders tend to be in similar functional pathways and these genes tend to have more functional interactions. In their biofilter approach for prioritizing genes for GWAS analysis, Bush et al. [] point out that epistasis may lead to a failure of replication of single-SNP effects. Specifically, the effect of one allele […]

library_books

Phenome Wide Association Study to Explore Relationships between Immune System Related Genetic Loci and Complex Traits and Diseases

2016
PLoS One
PMCID: 4980020
PMID: 27508393
DOI: 10.1371/journal.pone.0160573

[…] we selected only SNPs from our genome-wide array data that were on the ImmunoChip array or within the genes we identified for involvement in the immune system. The SNP filtering process is shown in .Biofilter was the tool used to generate the list of SNPs for association testing. Biofilter is a software tool with an extensive database containing biological knowledge from publicly available reposi […]

Citations

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Biofilter institution(s)
Center for Systems Genomics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University PA, USA; Eberly College of Science, The Pennsylvania State University, PA, USA; The Huck Institutes of the Life Sciences, PA, USA
Biofilter funding source(s)
Funded by the grants: 5R01 LM010040, U19 HL065962, U01 HG006389.

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