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CaptureCompendium: a comprehensive toolkit for 3C analysis.

Telenius, J. M.; Downes, D.; Sergeant, M.; Oudelaar, A. M.; McGowan, S.; Kerry, J.; Hanssen, L. L. P.; Schwessinger, R.; Eijsbouts, C. Q.; Davies, J. O. J.; Taylor, S.; Hughes, J. R.

2020-02-18 bioinformatics
10.1101/2020.02.17.952572 bioRxiv
Show abstract

DNA folding within nuclei is a highly ordered process, with implications for gene regulation and development. An array of chromosome conformation capture (3C) methods have been developed to investigate how DNA is packaged within nuclei and to interrogate specific interactions. While these methods use different approaches to examine target loci (many-versus-all) or the entire genome (all-versus-all), they all rely on the core principle of endonuclease digestion and proximity-based ligation to re-arrange genomic order to reflect the three-dimensional nuclear conformation. This sequence reorganization creates novel chimeric DNA fragments which require specialist bioinformatic tools to analyze and visualize. Despite this need for specialist bioinformatic skills, the core biological importance of genome folding has seen widespread methodological uptake. To service the needs of experimentalists using the many-versus-all Capture-C family of methods we have developed CaptureCompendium; a toolkit of software to simplify the design, analysis and presentation of 3C experiments.

Matching journals

The top 5 journals account for 50% of the predicted probability mass.

1
Nucleic Acids Research
◐ 1281 papers in training set
Top 0.9%
17.9%
Similar papers in this journal
2
Nature Communications
○ 5641 papers in training set
Top 15%
12.5%
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3
Nature Protocols
○ 33 papers in training set
Top 0.1%
11.5%
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4
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 0.4%
7.6%
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5
Bioinformatics
◐ 1204 papers in training set
Top 4%
6.0%
Similar papers in this journal
50% of probability mass above
6
Genome Biology
○ 637 papers in training set
Top 2%
5.3%
7
BMC Bioinformatics
○ 457 papers in training set
Top 2%
3.3%
8
Cell Reports Methods
○ 165 papers in training set
Top 0.5%
3.3%
9
Nature Methods
○ 385 papers in training set
Top 3%
3.1%
10
Briefings in Bioinformatics
◐ 354 papers in training set
Top 3%
3.0%
11
Scientific Reports
○ 3612 papers in training set
Top 39%
2.6%
12
BMC Genomics
○ 406 papers in training set
Top 3%
2.6%
13
Bioinformatics Advances
◐ 203 papers in training set
Top 3%
2.0%
14
Genome Research
● 468 papers in training set
Top 3%
1.8%
15
F1000Research
○ 88 papers in training set
Top 1%
1.8%
16
Nature Biotechnology
○ 172 papers in training set
Top 3%
1.6%
17
ACS Synthetic Biology
● 287 papers in training set
Top 2%
1.1%
18
GigaScience
◐ 212 papers in training set
Top 4%
1.0%
19
Life Science Alliance
● 285 papers in training set
Top 7%
0.9%
20
STAR Protocols
○ 18 papers in training set
Top 0.3%
0.8%
21
Communications Biology
○ 993 papers in training set
Top 32%
0.8%
22
PLOS Computational Biology
● 1863 papers in training set
Top 22%
0.6%
23
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 8%
0.6%
24
G3 Genes|Genomes|Genetics
◐ 351 papers in training set
Top 5%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.