Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
2 · The registry
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
5 · Who and what money
Authors and funding
23 authors.
David KainerComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0001-7271-4676
Matthew LaneComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0002-7750-6822
Kyle A SullivanComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0002-4621-5598
J Izaak MillerComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0002-6114-5401
Mikaela CashmanComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0003-0620-7830
Mallory MorganComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0002-3309-1813
Ashley CliffComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0001-7809-5546
Jonathon RomeroComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0001-5249-1946
Angelica WalkerComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0003-4308-6302
D Dakota BlairComputational Science Initiative, Brookhaven National Laboratory, PO Box 5000 Upton, NY 11973, USA.ORCID 0000-0001-9742-7585
Hari ChhetriComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0001-6820-8789
Yongqin WangComputational Science Initiative, Brookhaven National Laboratory, PO Box 5000 Upton, NY 11973, USA.ORCID 0000-0002-2336-1680
Mirko PavicicComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0002-2908-3183
Anna FurchesComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0002-7376-5923
Jaclyn NoshayComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0002-7438-193X
Meghan DrakeComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0001-7969-4823
A J IrelandDepartment of Crop and Soil Sciences, University of Georgia, Miller Plant Sciences Building 120 Carlton Street Athens GA 30602, USA.ORCID 0000-0003-1982-9065
Ali MissaouiComputational Science Initiative, Brookhaven National Laboratory, PO Box 5000 Upton, NY 11973, USA.ORCID 0000-0003-1710-1142
Yun KangNoble Research Institute, 2510 Sam Noble Parkway Ardmore, OK 73401, USA.ORCID 0000-0002-8556-4723
John C SedbrookSchool of Biological Sciences, Illinois State University, School of Biological Sciences Illinois State University Campus Box 4120 Normal, IL 61790, USA.ORCID 0000-0002-4930-1627
Paramvir DehalDepartment of Crop and Soil Sciences, University of Georgia, Miller Plant Sciences Building 120 Carlton Street Athens GA 30602, USA.ORCID 0000-0001-5810-2497
Shane CanonDepartment of Crop and Soil Sciences, University of Georgia, Miller Plant Sciences Building 120 Carlton Street Athens GA 30602, USA.ORCID 0000-0002-8440-738X
Daniel JacobsonComputational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.ORCID 0000-0002-9822-8251
Funding
DOEOak Ridge National Laboratory DE-AC05-00OR22725U.S. Department of Energy Office of Science DE-AC02-05CH11231
6 · The paper itself
Abstract
We introduce RWRtoolkit, a multiplex generation, exploration, and statistical package built for R and command-line users. RWRtoolkit enables the efficient exploration of large and highly complex biological networks generated from custom experimental data and/or from publicly available datasets, and is species agnostic. A range of functions can be used to find topological distances between biological entities, determine relationships within sets of interest, search for topological context around sets of interest, and statistically evaluate the strength of relationships within and between sets. The command-line interface is designed for parallelization on high-performance cluster systems, which enables high-throughput analysis such as permutation testing. Several tools in the package have also been made available for use in reproducible workflows via the KBase web application.
Indexed as
Computational BiologyGene Regulatory NetworksSoftwareAnimalsHumansMultiomicsmulti-omicmultiplex networkrandom walk with restartsoftware packagesystems biology
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species. · full record | OpenQuestion