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https://cran.r-project.org/package=rncl

Software R package provides interface to Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. Provides elements of file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'.

Proper citation: rncl (RRID:SCR_024290) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/hms/index.html

Software R package implements S3 class for storing and formatting time-of-day values, based on the 'difftime' class.

Proper citation: hms (RRID:SCR_024294) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/au/en/home/electron-microscopy/products/software-em-3d-vis/maps-software.html

Correlative electron microscopy and cross-platform imaging automation software. Imaging and correlative workflow software suite compatible with full line of Thermo Scientific SEM, DualBeam (FIB SEM) and TEM platforms.

Proper citation: Thermo Scientific Maps Software (RRID:SCR_024446) Copy   

•   Source: SciCrunch Registry

https://github.com/biod/sambamba

Software tools for working with SAM/BAM data

Proper citation: sambamba (RRID:SCR_024328) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/chrjan/seq-seq-pan

Software workflow for SEQuential alignment of SEQuences to build PAN-genome data structure and whole-genome-alignment.

Proper citation: seq-seq-pan (RRID:SCR_024343) Copy   

•   Source: SciCrunch Registry

https://github.com/losonczylab/sima

Software Python package for analysis of dynamic fluorescence microscopy data.

Proper citation: SIMA (RRID:SCR_024466) Copy   

•   Source: SciCrunch Registry

https://github.com/SciTools/cartopy

Software Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses. Cartographic library with matplotlib support.

Proper citation: Cartopy (RRID:SCR_024587) Copy   

•   Source: SciCrunch Registry

https://mc-stan.org/bayesplot/

Software R package providing extensive library of plotting functions for use after fitting Bayesian models.Plotting functions for posterior analysis, MCMC diagnostics, prior and posterior predictive checks, and other visualizations to support the applied Bayesian workflow.

Proper citation: bayesplot (RRID:SCR_024588) Copy   

•   Source: SciCrunch Registry

https://www.pacemweb.nl/simulation/assessment-settings

Web tool for aggregate consumer exposure assessment. Model is based on realistic product usage information obtained from surveys. Information on usage, frequency and amount of personal care products and household cleaning products in various European countries is included.

Proper citation: PACEMweb (RRID:SCR_023083) Copy   

•   Source: SciCrunch Registry

http://ml-neuronbrowser.janelia.org/

Interactive web platform for anyone to explore, search, filter and visualize the single neuron reconstructions.

Proper citation: MouseLight Neuron Browser (RRID:SCR_016669) Copy   

•   Source: SciCrunch Registry

http://fairbydesign.nl

Software metadata ingestion platform that helps to improve quality of metadata. Station allows users to record meta-data according to minimum information standards thereby ensuring FAIR scientific data management from the start.

Proper citation: FAIR Data Station (RRID:SCR_023239) Copy   

•   Source: SciCrunch Registry

https://www.piirus.com

A database and collaboration tool which allows researchers to make contacts or find collaborators within their field or from a different discipline. Users can create a profile detailing their collaboration interests, research areas, and methodologies as well as add links to external sites such as LinkedIn and Academia.edu. Piirus takes the information from users' profiles to suggest researchers with whom they may be interested in collaborating with. Users can also search for users with particular interests, expertise, or techniques.

Proper citation: Piirus (RRID:SCR_013964) Copy   

•   Source: SciCrunch Registry

https://github.com/linnarsson-lab/loom-viewer

Software tool for sharing, browsing and visualizing single-cell data stored in the Loom file format.

Proper citation: loom-viewer (RRID:SCR_016683) Copy   

•   Source: SciCrunch Registry

https://cell-innovation.nig.ac.jp/maser/Tools/visualization_top_en.html

One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGffToGe_db for custom genome software loads GFF files of custom genomes to a database for Genome Explorer. It allows the user to browse the results through the GE.

Proper citation: loadGffToGe_db for custom genome (RRID:SCR_015997) Copy   

•   Source: SciCrunch Registry

http://www.mricro.com

Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.

Proper citation: MRIcron (RRID:SCR_002403) Copy   

•   Source: SciCrunch Registry

https://developers.google.cn/earth-engine/

Web application as public data catalog, compute infrastructure, geospatial APIs and interactive app server. Geospatial processing service.

Proper citation: Google Earth Engine (RRID:SCR_023224) Copy   

•   Source: SciCrunch Registry

http://www.uchicagoddrcc.org

Center whose goals include fostering collaboration among basic and clinical investigators, facilitating the use of new technologies in the study of treatment of digestive diseases, and providing education and training for improved treatment and diagnosis.

Proper citation: University of Chicago Digestive Diseases Research Core Center (RRID:SCR_015601) Copy   

•   Source: SciCrunch Registry

http://openneu.ro/metasearch

Web application search tool intended to help users find MRI data shared publicly on the Web, particularly from projects organized under the 1000 Functional Connectomes Project (FCP) and International Neuroimaging Data-sharing Initiative (INDI). Users can perform queries visually to select a cohort of participants with brain imaging data based on their demographics and phenotypic information and then link out to imaging measures.

Proper citation: MetaSearch (RRID:SCR_014751) Copy   

•   Source: SciCrunch Registry

http://www.bsc.gwu.edu/dpp/index.htmlvdoc

Multicenter clinical research study aimed at discovering whether modest weight loss through dietary changes and increased physical activity or treatment with the oral diabetes drug metformin (Glucophage) could prevent or delay the onset of type 2 diabetes in study participants. At the beginning of the DPP, all 3,234 study participants were overweight and had blood glucose levels higher than normal but not high enough for a diagnosis of diabetesa condition called prediabetes. In addition, 45 percent of the participants were from minority groups-African American, Alaska Native, American Indian, Asian American, Hispanic/Latino, or Pacific Islander-at increased risk of developing diabetes. The DPP found that participants who lost a modest amount of weight through dietary changes and increased physical activity sharply reduced their chances of developing diabetes. Taking metformin also reduced risk, although less dramatically. In the DPP, participants from 27 clinical centers around the United States were randomly divided into different treatment groups. The first group, called the lifestyle intervention group, received intensive training in diet, physical activity, and behavior modification. By eating less fat and fewer calories and exercising for a total of 150 minutes a week, they aimed to lose 7 percent of their body weight and maintain that loss. The second group took 850 mg of metformin twice a day. The third group received placebo pills instead of metformin. The metformin and placebo groups also received information about diet and exercise but no intensive motivational counseling. A fourth group was treated with the drug troglitazone (Rezulin), but this part of the study was discontinued after researchers discovered that troglitazone can cause serious liver damage. The participants in this group were followed but not included as one of the intervention groups. In the years since the DPP was completed, further analyses of DPP data continue to yield important insights into the value of lifestyle changes in helping people prevent type 2 diabetes and associated conditions. For example, one analysis confirmed that DPP participants carrying two copies of a gene variant, or mutation, that significantly increased their risk of developing diabetes benefited from lifestyle changes as much as or more than those without the gene variant. Another analysis found that weight loss was the main predictor of reduced risk for developing diabetes in DPP lifestyle intervention group participants. The authors concluded that diabetes risk reduction efforts should focus on weight loss, which is helped by increased exercise.

Proper citation: Diabetes Prevention Program (RRID:SCR_001501) Copy   

•   Source: SciCrunch Registry

https://amstar.ca/

Guide tool to assess methodological quality of systematic reviews. Used to evaluate systematic reviews of randomised trials. AMSTAR 2 enables more detailed assessment of systematic reviews that include randomised or non-randomised studies of healthcare interventions, or both.

Proper citation: AMSTAR (RRID:SCR_023194) Copy   

•   Source: SciCrunch Registry