GENSENG protocols

GENSENG specifications

Information


Unique identifier OMICS_00345
Name GENSENG
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Jin P. Szatkiewicz <>

Publication for GENSENG

GENSENG IN pipelines

 (5)
2018
PMCID: 5831535
PMID: 29490610
DOI: 10.1186/s12859-018-2077-6

[…] windows and computed read-count in each window. we chose four window sizes (i.e., 100bps, 200bps, 500bps, and 1000bps) to generate four sets of read-count data. finally, we applied both genseng and r-genseng to each of the four read-count datasets. for r-genseng, we choose 0.99 for the sampling parameter h based on the fact that less than 1% of windows have cnv., using the implanted […]

2018
PMCID: 5831535
PMID: 29490610
DOI: 10.1186/s12859-018-2077-6

[…] and computed read-count in each window. we chose four window sizes (i.e., 100bps, 200bps, 500bps, and 1000bps) to generate four sets of read-count data. finally, we applied both genseng and r-genseng to each of the four read-count datasets. for r-genseng, we choose 0.99 for the sampling parameter h based on the fact that less than 1% of windows have cnv., using the implanted cnvs […]

2018
PMCID: 5831535
PMID: 29490610
DOI: 10.1186/s12859-018-2077-6

[…] four window sizes (i.e., 100bps, 200bps, 500bps, and 1000bps) to generate four sets of read-count data. finally, we applied both genseng and r-genseng to each of the four read-count datasets. for r-genseng, we choose 0.99 for the sampling parameter h based on the fact that less than 1% of windows have cnv., using the implanted cnvs as the ground truth, we calibrated the sensitivity and false […]

2018
PMCID: 5831535
PMID: 29490610
DOI: 10.1186/s12859-018-2077-6

[…] for the sampling parameter h based on the fact that less than 1% of windows have cnv., using the implanted cnvs as the ground truth, we calibrated the sensitivity and false discovery rate (fdr) of r-genseng in comparison to genseng. following [10], a true discovery is a reported cnv that satisfies two conditions: 1) having ≥50% reciprocal overlap with the ground truth cnv, and 2) […]

2018
PMCID: 5831535
PMID: 29490610
DOI: 10.1186/s12859-018-2077-6

[…] h based on the fact that less than 1% of windows have cnv., using the implanted cnvs as the ground truth, we calibrated the sensitivity and false discovery rate (fdr) of r-genseng in comparison to genseng. following [10], a true discovery is a reported cnv that satisfies two conditions: 1) having ≥50% reciprocal overlap with the ground truth cnv, and 2) having the same type (deletion […]

GENSENG institution(s)
Department of Genetics, University of North Carolina, Chapel Hill, NC, USA

GENSENG reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GENSENG