BCRANK protocols

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BCRANK specifications

Information


Unique identifier OMICS_15781
Name BCRANK
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.42.0
Stability Stable
Requirements
methods, Biostrings, seqLogo
Maintained Yes

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  • person_outline Adam Ameur <>

BCRANK in pipeline

2016
PMCID: 4964843
PMID: 27516766
DOI: 10.3389/fpls.2016.01125

[…] genes were identified by filtering the rna-seq data with the following cut-off:two ratio in expression level and false discovery rate (fdr) of less than 0.05., a motif search was performed using bcrank package of r software (ameur et al., ). this method takes a ranked list of genomic regions as input and outputs short dna sequences that are overrepresented in some part of the list. […]


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BCRANK in publications

 (9)
PMCID: 5154163
PMID: 27964748
DOI: 10.1186/s13073-016-0382-0

[…] have generally been used to identify binding sites and the strength of binding; however, recent studies have examined the actual sequences themselves, to identify variants that affect dna binding. bcrank is an algorithm designed to detect regulatory snps (regsnps) in chip-chip data based upon snp genotyping in dna-binding sites []. more recently, another strategy used chip-seq data to nominate […]

PMCID: 5137168
PMID: 27917918
DOI: 10.1038/srep38411

[…] gene expression patterns were clustered using the k-means algorithm in genespring. common promoter motifs from 5000 bp upstream of the genes included in each k-means cluster were extracted using the bcrank package., gene expression was quantified as reads per kilobase of candidates per million mapped reads (rpkm), calculated by dividing cdpv by the respective gene lengths expressed in kilobase […]

PMCID: 4964843
PMID: 27516766
DOI: 10.3389/fpls.2016.01125

[…] genes were identified by filtering the rna-seq data with the following cut-off:two ratio in expression level and false discovery rate (fdr) of less than 0.05., a motif search was performed using bcrank package of r software (ameur et al., ). this method takes a ranked list of genomic regions as input and outputs short dna sequences that are overrepresented in some part of the list. […]

PMCID: 4770861
PMID: 26928673
DOI: 10.3402/jev.v5.30924

[…] their putative promoters and then we tested if any tf binding site is enriched in these regions. in parallel, we used a variety of motif enrichment tools available in r/bioconductor (cosmo, bcrank, motifrg) to find short motifs enriched in secreted mirnas. results: we found that no specific tf binding site is enriched in the promoters of secreted mirnas. however, we identified 2 short […]

PMCID: 4620995
PMID: 26526876
DOI: 10.4137/EBO.S25585

[…] from geo database directly into r; genenet version 1.2.12 to model the grn; graphviz version 2.38, dnet version 1.0.7, venerable version 3.0, and igraph version 0.7.1 for network visualization; and bcrank version 1.26.0. the detailed computational pipeline used for the analyses is presented in supplementary file s02. the r source code for the analyses is provided in supplementary file s03., […]


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