CircTest protocols

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CircTest specifications

Information


Unique identifier OMICS_10568
Name CircTest
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data CircTest is strongly recommended to work with the output of DCC.
Output data Some candidate circles.
Operating system Unix/Linux
Programming languages Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.1.0
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Christoph Dieterich <>

Publication for CircTest

CircTest in pipelines

 (2)
2018
PMCID: 5753478
PMID: 29298683
DOI: 10.1186/s12864-017-4386-y

[…] values were corrected for multiple hypothesis testing with fdr < 0.2. to identify stage-specific circrnas (fig. ), and for pair-wise comparisons of host gene expression independent changes using circtest [] (fig. ), we required a minimum of 6 reads per time-point., the circtest pipeline was implemented to test for host gene independent circrnas []. dcc 0.0.4 […]

2016
PMCID: 4996846
PMID: 27132142
DOI: 10.1016/j.gpb.2016.02.003

[…] several experimental conditions and replicates. dcc analysis took place with version 0.3.2 using the parameters “-m -nr 2 2 -fg -g -f -l 20”. further statistical analyses were performed with the circtest r package provided with dcc and additional custom-tailored perl scripts., cd designed the study; lc and rr performed all rna and sequencing experiments. tj and cd analysed the data and wrote […]


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CircTest in publications

 (3)
PMCID: 5753478
PMID: 29298683
DOI: 10.1186/s12864-017-4386-y

[…] versus their counterpart linear rna changes from the same host gene (fig. ). for this analysis, we used an expanded list of circrnas, requiring at least 6 reads per age time-point. using the circtest algorithm [], we tested for statistically significant changes in circrna expression independent of host gene expression. from 1239 circrnas tested, 459 showed a host gene independent […]

PMCID: 4931246
PMID: 27350239
DOI: 10.1038/ncomms12060

[…] for exons that were constitute or absent in mrnas, their ψ values were recorded as 1 or 0, respectively. we performed statistical tests based on a β-binomial model, adapted from a previous approach (circtest), except that we replaced the observed read counts from linear or circular isoforms with those from circular transcript splicing in or out of a detected exon. for each pair of the four […]

PMCID: 4996846
PMID: 27132142
DOI: 10.1016/j.gpb.2016.02.003

[…] dcc software was used to identify circrna candidates from chimeric read mappings (see materials and methods). this initial step yielded 8375 potential circrna regions. we subsequently employed the circtest suite in dcc to confine the search to 741 circrna loci by filtering for consistent read support and a minimal proportion of junction-spanning reads (1%). lastly, we tested enrichment […]


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CircTest institution(s)
Max Planck Institute for Biology of Ageing, Cologne, Germany
CircTest funding source(s)
The Max Planck Society

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