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http://cran.r-project.org/web/packages/gap/
GAP is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.
Proper citation: Genetic Analysis Package (RRID:SCR_003006) Copy
https://code.google.com/p/sasqpcr/
All-in-one computer program for robust and rapid analysis of quantitative reverse transcription real-time polymerase chain reaction (RT-qPCR) data in SAS. It incorporates all functions important for RT-qPCR data analysis including assessment of PCR efficiencies, validation of internal reference genes and normalizers, normalization of confounding variations across samples and statistical comparisons of target gene expression in parallel samples. The program is highly automatic in data analyses and result output. The input data have no limitations for the number of genes or cDNA samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. The program is also extendable allowing advanced SAS users to develop particular statistical tests appropriate for their experimental designs. Thus users are the actual decision-makers controlling RT-qPCR data analyses. The program has to be used in SAS software; however, extensive SAS programming knowledge is not required.
Proper citation: SASqPCR (RRID:SCR_003056) Copy
http://sourceforge.net/projects/molbiolib/
A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++.
Proper citation: MolBioLib (RRID:SCR_005372) Copy
A genome browser specialized in next-generation sequencing data.
Proper citation: GenomeJack (RRID:SCR_012026) Copy
Specializes in sequence and array-based SNP and copy number analysis, genetic association software, and analytic services. Their technologies empower scientists to determine the genetic causes of disease, transform drug discovery, develop genetic diagnostics, and advance the quest for personalized medicine.
Proper citation: Golden Helix Incorporated (RRID:SCR_012191) Copy
http://www.patternlabforproteomics.org/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. Gene Ontology Explorer (GOEx) combines data from protein fold changes with GO over-representation statistics to help draw conclusions in proteomic experiments. It is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alternative strategy, there will be no protein fold information. Platform: Windows compatible
Proper citation: GOEx - Gene Ontology Explorer (RRID:SCR_005779) Copy
https://www.thermofisher.com/order/catalog/product/00-0210
Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis.
Proper citation: GeneChip™ Scanner 3000 7G (RRID:SCR_016522) Copy
Commercially provides services and products for research in the fields of molecular biology, diagnostics, enzymes and proteins.
Proper citation: NZYTech (RRID:SCR_016772) Copy
https://bionanogenomics.com/wp-content/uploads/2017/01/30047-Irys-User-Guide.pdf
System by BioNano Genomics ( formerly BioNanomatrix) which provides optical next generation mapping (NGM). Used for sequence assembly and structural variation analysis. Provides Scaffold Bionano genome mapping data with sequencing data to improve assembly contiguity, reduce sequencing coverage needed, and automatically correct errors in sequencing based assemblies.
Proper citation: BioNano Irys system (RRID:SCR_016754) Copy
https://www.scanco.ch/microct100.html
Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG.
Proper citation: SCANCO Medical microCT 100 system (RRID:SCR_017119) Copy
https://www.agilent.com/cs/library/usermanuals/Public/G2505-90019_ScannerC_User.pdf
Microarray Scanner is part of microarray analysis solution from Agilent Technologies. Laser induced fluorescence scanner designed to read microarrays printed on standard slides. Measures fluorescence intensity of labeled sample nucleic acid bound to microarrays.
Proper citation: Agilent G2565CA Microarray Scanner (RRID:SCR_017206) Copy
https://www.leica-microsystems.com/products/microscope-software/details/product/leica-las-x-ls/
Software for image capture, processing and analysis with Leica fluorescence and confocal microscopes.
Proper citation: Leica Application Suite X (RRID:SCR_013673) Copy
http://www.cyto.purdue.edu/flowcyt/software/Winmdi.htm
Software to analyze flow cytometry listmode data files.
Proper citation: WinMDI Software (RRID:SCR_013745) Copy
A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure.
Proper citation: Jalview (RRID:SCR_006459) Copy
http://bioconductor.org/packages/2.9/bioc/html/RamiGO.html
Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.
Proper citation: RamiGO (RRID:SCR_006922) Copy
https://www.mangold-international.com/en/products/software/behavior-research-with-mangold-interact
Software platform for synchronized viewing and analysis of video footage and audio files in observational research by Mangold International GmbH. Qualitative and quantitative video coding software.
Proper citation: Interact (RRID:SCR_019254) Copy
Automatic Methane Potential Test System (AMPTS) II is analytical tool for conducting various anaerobic batch fermentation tests. This includes performing, with up to 15 test vials, biochemical methane potential (BMP) tests, anaerobic biodegradability studies, specific methanogenic activity (SMA) assays, as well as conducting residual gas potential (RGP) analyses on digested slurry.
Proper citation: Biomethane Potential Test (RRID:SCR_017319) Copy
Developer of medical software to offer image analysis technologies. Company in Denmark that provides medical image processing software to get quantifiable and accurate insight into brain.
Proper citation: Brainreader (RRID:SCR_017308) Copy
https://www.labx.com/item/molecular-devices-molecular-dynamics-storm-860-molecular/3896212
Multifunction phosphoimager fluorimager laser scanner that collects fluorescent or storage phosphor images from gels, membranes and phosphor screens. It is equipped with blue (450 nm) and red (635 nm) lasers, can scan at resolutions down to 50 microns. It is able to quantify radioactive gels for commonly used isotopes such as 32P, 33P, 125I, 35S, and 14C. There are three detection modes: phosphor screen mode, red/blue fluorescence, chemifluorescence.
Proper citation: Molecular Dynamics Storm 860 Molecular Imager (RRID:SCR_018032) Copy
https://www.rcon-ndt.com/wp-content/uploads/Nanotom.pdf
System for scientific and industrial nanofocus computed tomography nanoCT and 3D metrology. Realizes unique spatial and contrast resolution on wide sample and application range. Used in material science, precision injection moulding, micromechanics, electronics geology and biology. Used in 3D CT applications. Allows many analysis, e.g. non-destructive visualization of slices, arbitrary sectional views, or automatic pore analysis.
Proper citation: Phoenix Nanotom S (RRID:SCR_017995) Copy
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