TADbit specifications

Information


Unique identifier OMICS_11390
Name TADbit
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data TADbit takes as input the sequencing reads of 3C-based experiments.
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.2.51
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Guillaume Filion <>
  • person_outline Marc Marti-Renom <>

Additional information


http://3dgenomes.github.io/TADbit/

Publications for TADbit

TADbit in publications

 (9)
PMCID: 5928121
PMID: 29712907
DOI: 10.1038/s41467-018-04130-x

[…] the overlap between the two was computed with custom r scripts using the package genomicranges., to compute the rates of contact decay, the raw hi-c reads were normalized in 50 kb windows using the tadbit pipeline with default parameters. the contact decays were estimated using a simple linear regression between the logarithm of the linear separation between the windows and the logarithm […]

PMCID: 5910504
PMID: 29686798
DOI: 10.1016/j.csbj.2018.02.003

[…] calling. for example, tadtool (as a python package) enables the direct export of tads called using a set of parameters for both directionality and insulation indices []. other tad callers, such as tadbit [], armatus [], and tadtree [], exhibit balanced performance for most parameters for experimental and simulated data. interaction callers, such as homer [] and hiccups, [,] yield the highest […]

PMCID: 5700980
PMID: 29170434
DOI: 10.1038/s41467-017-01962-x

[…] sizes larger than 150 nm obtained from chip-seq vs. microscopy imaging. changes in this threshold did not affect our main conclusions., hi-c data were processed using an in-house pipeline based on tadbit. first, the quality of the reads was checked using the quality_plot() function in tadbit, which is similar to the tests performed by the fastqc program with adaptations for hi-c data sets. […]

PMCID: 5638070
PMID: 28771695
DOI: 10.1002/1873-3468.12778

[…] software can also read and analyze 3c‐based interaction data by converting experimental reads into a tool‐specific hi‐c format, which can then be visualized using the juicebox browser . finally, the tadbit software can output complete experimental dataset in standard json format, which can then be imported and visualized using the tadkit 3d browser. importantly, data accessibility […]

PMCID: 5504709
PMID: 28693562
DOI: 10.1186/s13072-017-0142-4

[…] as a measure of the model quality, we used the spearman’s correlation coefficient between the modeled matrix of interactions and the experimental 5c matrix (additional file : figure s4). the tadbit program (https://github.com/3dgenomes/tadbit) was used for all calculations. chimera [] and pymol (the pymol molecular graphics system, version 1.7.4 schrodinger, llc), tools were used […]


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TADbit institution(s)
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Barcelona, Spain
TADbit funding source(s)
Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement 609989, the Spanish Ministry of Economy and Competitiveness (BFU2013-47736- P) and the Human Frontiers Science Program (RGP0044) and the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208 to the CRG.

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