Babel statistics

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Babel specifications

Information


Unique identifier OMICS_01530
Name Babel
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 0.3-0
Stability Stable
Requirements
parallel, edgeR, R(≥2.14.0), R.rsp, R.devices, R.utils
Maintained Yes

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Documentation


Maintainer


  • person_outline Adam B. Olshen <>

Publication for Babel

Babel in publications

 (5)
PMCID: 5473967
PMID: 28622766
DOI: 10.1186/s13059-017-1222-2

[…] identify the true-positive ‘translation only’ cycling transcripts with higher reliability, we implemented the same methodology as in our previous study []. briefly, we used the analytical framework babel [] to preselect all transcripts whose translation efficiency changed significantly over the day (and/or whose tes deviated significantly from the global transcript population). rhythmicity […]

PMCID: 5507668
PMID: 28635594
DOI: 10.7554/eLife.27786.024

[…] mapping sites and cds annotation was calculated by using the intersectbed function of bedtools., gene-level translation efficiency between each pair of adjacent stages was quantified by using the babel analytical method (). genes with empirical p-values<0.05 at any of the stages were considered to have differentially regulated translation efficiency. the translation efficiency […]

PMCID: 5314775
PMID: 27923997
DOI: 10.1093/nar/gkw1190

[…] riboseq data, and tisdb () is a collection of translation initiation sites predicted from riboseq data. several stand alone tools were developed for differential gene expression analysis (anota (), babel (), ribodiff (), xtail ()), and for the prediction of translated orfs (ribotaper (), orf-rator () and ribohmm ()). ribomap () estimates footprint origins in the presence of multiple splice […]

PMCID: 4832044
PMID: 27114907
DOI: 10.1016/j.gdata.2016.03.004

[…] of counted reads per 1000 mapped and counted bases per geometric mean of normalized read counts per million (rpkm). translation efficiencies were calculated as the ratio of rpf-rpkm/mrna rpkm. the babel framework was used to assess significant changes in translational regulation . we used a mixed model approach for rhythmicity detection (sigmoid and sinusoidal curve fittings). rhythmic […]

PMCID: 4700579
PMID: 26729373
DOI: 10.1186/s12864-015-2354-y

[…] genes, were likely de novo translational targets of mtorc1 signaling because they responded strongly to 3 h treatment., previous analysis by another group using a bioinformatics approach known as babel analysis identified genes with significantly reduced translation associated with impeded mtor activity []. in addition to the prte and 5’top genes, this group of genes includes subunits […]


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Babel institution(s)
Department of Epidemiology and Biostatistics, Helen Diller Family Comprehensive Cancer Center, Department of Medicine and Department of Urology, University of California, San Francisco, CA, USA; Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, USA

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