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Protocols

OpenMEE specifications

Information


Unique identifier OMICS_24443
Name OpenMEE
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, R
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 0.3.3
Stability Stable
Source code URL https://codeload.github.com/kundajelab/chipseq_pipeline/tar.gz/0.3.3
Maintained Yes

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Versioning


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Maintainers


  • person_outline Jessica Gurevitch
  • person_outline Byron Wallace

Publication for OpenMEE

OpenMEE citations

 (4)
library_books

Platelet to lymphocyte ratio in the setting of liver transplantation for hepatocellular cancer: A systematic review and meta analysis

2018
PMCID: 5910549
PMID: 29686473
DOI: 10.3748/wjg.v24.i15.1658

[…] ence intervals (CI) > 1 revealed that the patients with high PLR values had poor prognoses (higher risk of recurrence), whereas a result < 1 had the opposite meaning. The analysis was performed using OpenMEE software (http://www.cebm.brown.edu/openmee/index.html). […]

library_books

Bi directional plasticity: Rotifer prey adjust spine length to different predator regimes

2017
Sci Rep
PMCID: 5579284
PMID: 28860451
DOI: 10.1038/s41598-017-08772-7

[…] e number is high enough (>5 N + 10, where N is the number of experiments), the analysis can be considered to be robust with respect to publication bias. All analyses were conducted using the software OpenMEE Windows 8. […]

call_split

The underestimated role of temperature–oxygen relationship in large‐scale studies on size‐to‐temperature response

2017
Ecol Evol
PMCID: 5606864
PMID: 28944028
DOI: 10.1002/ece3.3263
call_split See protocol

[…] species within a stream group we estimated a coefficient of regression for the size‐temperature relationship and we conducted the effect‐size analyzes of grand mean for r, using a meta‐analysis tool (OpenMEE software, Wallace et al., ), for each stream group separately. We used a fixed‐effect model for Fisher's Z‐transformed effect size. […]

library_books

Cover crops support ecological intensification of arable cropping systems

2017
Sci Rep
PMCID: 5291223
PMID: 28157197
DOI: 10.1038/srep41911

[…] among both crops and the four production systems, bare fallow to cover crop mean response ratios were calculated, as well as their 95% confidence interval (CI) values, with the meta-analysis program OpenMEE. Linear regressions were performed to test for effects of weed and N input on yield. Yield data were standardized per experiment and crop by creating a standardized yield (z-transformation) di […]

Citations

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OpenMEE institution(s)
College of Computer and Information Science, Northeastern University, Boston, MA, USA; 2 Department of Integrative Biology, University of South Florida, FL, USA; 3 Center for Evidence-Based Medicine, School of Public Health, Brown University, Providence, RI, USA; 4 Department of Health Services, Policy & Practice, School of Public Health, Brown University, Providence, RI, USA; 5 Department of Biostatistics, School of Public Health, Brown University, Providence, RI, USA; and 6 Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
OpenMEE funding source(s)
Supported by National Science Foundation grants DBI-1262402, DBI-1262442, and DBI-1262545.

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