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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://CRAN.R-project.org/package=simr
Software R package for power analysis of generalized linear mixed models by simulation. Used to calculate power for generalised linear mixed models.
Proper citation: SIMR (RRID:SCR_019287) Copy
http://metagenomics.iiserb.ac.in/mp3/
Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MP3 tool (RRID:SCR_019282) Copy
https://labsn.github.io/expyfun/index.html
Auditory and visual stimulus delivery library for psychoacoustics in Python.
Proper citation: Expyfun (RRID:SCR_019285) Copy
https://CRAN.R-project.org/package=gbs2ploidy
Software R package as functions for inference of ploidy from Genotyping By Sequencing data, including function to infer allelic ratios and allelic proportions in Bayesian framework.
Proper citation: gbs2ploidy (RRID:SCR_019290) Copy
https://qiwei.shinyapps.io/PredictCOVID19/
Web app to help assess both short- and long-term forecasts of COVID-19 across the United States at multiple levels. Done by implementing one time-series model (ARIMA), one compartmental models (basic SIR), and six classical growth models, which all yield satisfactory prediction results in the past and current pandemics at early stage.
Proper citation: BayesEpiModels Web App (RRID:SCR_019292) Copy
https://github.com/pavanvidem/chira
Software tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.
Proper citation: ChiRA (RRID:SCR_019219) Copy
Web application for visualisation of information derived from residue contact predictions in combination with other sources of information, such as secondary structure predictions, transmembrane helical topology, sequence conservation.Provides interactive interface for researchers in field of protein bioinformatics that are interested in analysing data on given protein.
Proper citation: ConPlot (RRID:SCR_019216) Copy
https://github.com/bgcarlisle/TRNscreener
Software tool as R script to provide function that takes two arguments: path to folder of plain text files named by their DOI, and output filename. For each file in folder, it searches for trial identifiers based on regex matching and writes CSV that contains all trial registration numbers and in case of ClinicalTrials.gov entries, whether they correspond to registry entry on ClinicalTrials.gov.
Proper citation: Trial Registration Number screener (RRID:SCR_019211) Copy
https://CRAN.R-project.org/package=spdep
Software R package as collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree.
Proper citation: spdep (RRID:SCR_019294) Copy
https://CRAN.R-project.org/package=scales
Software R package as scale functions for visualization. Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.
Proper citation: scales (RRID:SCR_019295) Copy
Online SPE System automates solid phase extraction to enrich analytes, remove matrix components or lower detection limits.
Proper citation: Agilent: 1290 Infinity II Online SPE System (RRID:SCR_019380) Copy
https://www.agilent.com/en/products/atomic-absorption/atomic-absorption-systems/240z-aa
Atomic Absorption System is used for detection limits and analyzes difficult matrices.
Proper citation: Agilent: 240Z AA Atomic Absorption System (RRID:SCR_019385) Copy
Preparative LC/MSD System enables high throughput purification and delivers high quality compounds.
Proper citation: Agilent: 1290 Infinity II Preparative LC/MSD System (RRID:SCR_019381) Copy
https://www.agilent.com/en/products/mp-aes/mp-aes-systems/4100-mp-aes
Discontinued Superseded by 4210 MP AES System.
Proper citation: Agilent: 4100 MP-AES (RRID:SCR_019390) Copy
https://bioconductor.org/packages/synergyfinder/
Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations.
Proper citation: SynergyFinder (RRID:SCR_019318) Copy
https://www.agilent.com/en/products/mp-aes/mp-aes-systems/4200-mp-aes
High sensitivity atomic emission spectrometer. MP-AES Instrument utilizes microwave plasma and as it runs on air instead of combustible gases, it can be installed in either centralized laboratory or remote location. Detection limits down to ppb levels and no sample pretreatment necessary.
Proper citation: Agilent: 4200 MP-AES (RRID:SCR_019396) Copy
https://www.agilent.com/en/products/atomic-absorption/atomic-absorption-systems/240fs-aa
Atomic Absorption System determines the concentration of all elements from a single aspiration.
Proper citation: Agilent: 240FS AA Atomic Absorption System (RRID:SCR_019397) Copy
https://www.agilent.com/en/products/mp-aes/mp-aes-systems/4210-mp-aes
MP-AES provides detection limits and large linear dynamic range.
Proper citation: Agilent: 4210 MP-AES (RRID:SCR_019399) Copy
https://www.agilent.com/cs/library/datasheets/public/5991-6034EN.pdf
Micro GC System is used for gas analysis and offers comprehensive system control, data acquisition and report generation..
Proper citation: Agilent: 490 Micro GC System (RRID:SCR_019404) Copy
https://www.agilent.com/cs/library/usermanuals/public/G3582-90000.PDF
Micro GC Biogas Analyzer is used to analyze biogas and related sample streams and provide results.
Proper citation: Agilent: 490 Micro GC Biogas Analyzer (RRID:SCR_019405) Copy
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
