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bPeaks specifications

Information


Unique identifier OMICS_18991
Name bPeaks
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 1.2
Stability No
Source code URL https://cran.r-project.org/src/contrib/bPeaks_1.2.tar.gz
Maintained No

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Additional information


http://bpeaks.gene-networks.net/datafiles/bPeaks-manual.pdf

Publication for bPeaks

bPeaks citations

 (5)
library_books

Measurement of protein backbone 13CO and 15N relaxation dispersion at high resolution

2017
PMCID: 5626786
PMID: 28864905
DOI: 10.1007/s10858-017-0127-4

[…] may allow resolving signals overlapped in either 15n or 13co dimensions. however, we did not try this in our work., table 2 aas gauged by visual inspection of the spectra drawn at the noise level bpeaks corresponding to the amide groups of residues l13, d17, d32 and l43 cpeaks corresponding to the amide groups of residues y08 and l18 , aas gauged by visual inspection of the spectra drawn […]

library_books

The CCAAT Binding Complex Controls Respiratory Gene Expression and Iron Homeostasis in Candida Glabrata

2017
PMCID: 5471220
PMID: 28615656
DOI: 10.1038/s41598-017-03750-5

[…] of the ips, input dnas and mock ips samples and primary data analyses (quality controls and mapping of the reads) were performed as described previously. peak calling was performed with the bpeaks software, using both the input dna and the mock ip as references. for peak calling using the input dna as reference, the bpeaks parameters were t1 = 1.9, t2 = 6, t3 = 1, t4 = 0.7. for peak […]

library_books

Predicting floods with Flickr tags

2017
PMCID: 5325575
PMID: 28235035
DOI: 10.1371/journal.pone.0172870

[…] daily volume of pictures uploaded to the yahoo! flickr platform) as five days; however, there is scope for future data inquiries to adapt such periods for variable socio-environmental conditions: bpeaks=(nall-npeaksnpeaks)12(1), to identify whether the yahoo! flickr dataset contains elements with forecasting capacity vis-a-vis developing flooding events, we use a deconstructed cascade […]

library_books

A Network of Paralogous Stress Response Transcription Factors in the Human Pathogen Candida glabrata

2016
PMCID: 4860858
PMID: 27242683
DOI: 10.3389/fmicb.2016.00645

[…] averaged before the peak calling step, except for cgyap5 for which one of the two replicates had poor read coverage and was not used for further analyses. peak calling was performed with the bpeaks software (merhej et al., ), using both the input dna and the mock ip as references. for peak calling using the input dna as reference, the bpeaks parameters were t1 = 2, t2 = 2, t3 = 1.5, t4 = […]

library_books

The chaperone DnaK controls the fractioning of functional protein between soluble and insoluble cell fractions in inclusion body forming cells

2006
PMCID: 1555604
PMID: 16893469
DOI: 10.1186/1475-2859-5-26

[…] it was absent in thermal aggregates. according to previous analysis [] this peak corresponds to native-like species, that could be accounted by β-galactosidase moieties., adata are from figure 3, bpeaks at 1627 cm-1 and 1692 cm-1 can be attributed to extended intermolecular β-sheet while that at 1652 to disordered structure and/or α-helix., the formation of β-galactosidase thermal aggregates […]


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bPeaks institution(s)
Sorbonne Universités, UPMC University of Paris 06, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France; CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France; Ecole Normale Supérieure, Institut de Biologie de l’ENS (IBENS), Inserm U1024 and CNRS UMR 8197, Paris, France; Sorbonne Universités, UPMC University of Paris 06, UMR 7622, Laboratoire de Biologie du Développement, Paris, France; CNRS, UMR 7622, Laboratoire de Biologie du Développement, Paris, France; Institut Jacques Monod, CNRS UMR 7592, University of Paris Diderot, Paris, France
bPeaks funding source(s)
Supported by the STRUDYEV project of the French National Research Agency (ANR; Grant No. ANRJCJC-2010); by an ANR post-doctoral fellow hired in the frame of the STRUDYEV project; the Genomic Paris Centre IBENS platform, member of ‘France Génomique’ (Grant No. ANR10-INBS-09-08); by the program ‘Investissements d’Avenir’ launched by the French Government and implemented by the ANR (references ANR-10-LABX-54 MEMO LIFE and ANR-11-IDEX-0001-02 PSL* Research University).

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