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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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Versioning


No version available

Documentation


Maintainers


  • person_outline Guillaume Filion
  • person_outline Marc Marti-Renom

Additional information


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

Publications for TADbit

TADbit citations

 (9)
library_books

Theoretical principles of transcription factor traffic on folded chromatin

2018
Nat Commun
PMCID: 5928121
PMID: 29712907
DOI: 10.1038/s41467-018-04130-x

[…] rs. 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 of the […]

library_books

Computational Methods for Assessing Chromatin Hierarchy

2018
Comput Struct Biotechnol J
PMCID: 5910504
PMID: 29686798
DOI: 10.1016/j.csbj.2018.02.003

[…] AD 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 pr […]

call_split

Single cell absolute contact probability detection reveals chromosomes are organized by multiple low frequency yet specific interactions

2017
Nat Commun
PMCID: 5700980
PMID: 29170434
DOI: 10.1038/s41467-017-01962-x
call_split See protocol

[…] 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. Next […]

library_books

Challenges for visualizing three‐dimensional data in genomic browsers

2017
FEBS Lett
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 and portabilit […]

library_books

Activation of the alpha globin gene expression correlates with dramatic upregulation of nearby non globin genes and changes in local and large scale chromatin spatial structure

2017
PMCID: 5504709
PMID: 28693562
DOI: 10.1186/s13072-017-0142-4

[…] nalysis. 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 to visua […]

library_books

Defined chromosome structure in the genome reduced bacterium Mycoplasma pneumoniae

2017
Nat Commun
PMCID: 5344976
PMID: 28272414
DOI: 10.1038/ncomms14665

[…] me based on the filtered and normalized 10 kb resolution Hi-C matrix. Briefly, based on the hypothesis that chromatin interaction frequencies are a proxy for spatial proximities between loci, we used TADbit to convert the contact frequencies of genomic loci into spatial distances. Then we searched for the 3D conformations that best satisfied the spatial distances between genomic loci inferred from […]

Citations

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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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