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Citations per year

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

This map represents all the scientific publications referring to BCRANK per scientific context
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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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Maintainer


  • person_outline Adam Ameur

BCRANK citations

 (6)
library_books

Non coding single nucleotide variants affecting estrogen receptor binding and activity

2016
Genome Med
PMCID: 5154163
PMID: 27964748
DOI: 10.1186/s13073-016-0382-0

[…] ds 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 […]

library_books

Distinct epigenomes in CD4+ T cells of newborns, middle ages and centenarians

2016
Sci Rep
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 pair […]

library_books

Comparative Transcriptional Profiling of Primed and Non primed Rice Seedlings under Submergence Stress

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

[…] ulated 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. The algori […]

library_books

The 2nd UK Extracellular Vesicle Forum Meeting Abstracts

2016
J Extracell Vesicles
PMCID: 4770861
PMID: 26928673
DOI: 10.3402/jev.v5.30924

[…] dentified 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 mo […]

library_books

Differential binding and co binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP seq

2009
Genome Biol
PMCID: 3091322
PMID: 19919681
DOI: 10.1186/gb-2009-10-11-r129

[…] . Genes with a FOXA binding within 1 kb of their TSS demonstrated significantly higher expression than all genes (Figure S3 in Additional data file 1). A search with the de novo motif finding program BCRANK [] resulted in different motifs with variations of TGTTTAC as the top three for FOXA1 and top eight for FOXA3 (Figure ).As mentioned, members in the FOXA family regulate common pathways. This w […]

library_books

Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3

2008
BMC Genomics
PMCID: 2631581
PMID: 19087243
DOI: 10.1186/1471-2164-9-601

[…] As stated above, we also found strong support for hypothesis a), i.e. that the sequence of the Mig1 site is important for the degree of redundant repression. Thus, using the BCRANK program (see Methods), we found that a variant of the Mig1 site, GTGGGG(A/G/T)(A/T)G, is significantly enriched (p-value 9.4e-5) in the promoters of the redundantly repressed genes (Figure ). I […]


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