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on page 1 showing 20 out of 700 results

Cite this (16p_resource Code, RRID:SCR_016845)

URL: http://www.github.com/kmuench/16p_resource

Resource Type: Resource, software resource, source code

Software tool as a code to support figure generation for the manuscript by Roth, Muench et al. Used to perform analysis.

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Cite this (Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal, RRID:SCR_003743)

URL: http://www.type2diabetesgenetics.org/

Resource Type: Resource, disease-related portal, topical portal, database, service resource, portal, storage service resource, data repository, data or information resource

Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease.

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Cite this (Acquisition and Analysis for Electron Tomography, RRID:SCR_000192)

URL: http://www.biochem.mpg.de/en/rd/baumeister/research/ContentCEM/Software_development

Resource Type: Resource, software resource, software toolkit

A software platform for low dose electron tomography (ET) for all processing steps: acquisition, alignment, reconstruction, and analysis. Requires: Matlab R2008a and Image Processing Toolbox (V6.1)

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    ADAPT

Cite this (ADAPT, RRID:SCR_006769)

URL: http://bmsr.usc.edu/software/adapt/

Resource Type: Resource, software resource, software application, simulation software, data processing software, data analysis software

Computational modeling platform developed for pharmacokinetic and pharmacodynamic applications. It is intended for basic and clinical research scientists and is designed to facilitate the discovery, exploration and application of the underlying pharmacokinetic and pharmacodynamic properties of drugs. Features in ADAPT 5
*Individual Analysis ** Estimation module (ID) includes weighted least squares, maximum likelihood (ML), generalized least squares (GLS), maximum a posterior Bayesian estimation (MAP) ** Simulation module (SIM) includes capabilities for single and multisubject simulations ** Sample schedule design module (SAMPLE) provides the ability to calculate D- and C-optimal designs * Population Analysis ** Parametric population PK/PD modeling using maximum likelihood estimation via the EM algorithm with sampling (MLEM), as introduced by Schumitzky (1995) and by Walker (1996), with extensions and enhancements by Bauer & Guzy (2004). ** Iterated two-stage (ITS) analysis as proposed by Prevost (1977) and Steimer, Mallet and colleagues (1984). ** Convenient standard two-stage (STS) and naive pooled data (NPD) modeling, each with WLS, ML, and MAP estimators. System Requirements * Operating System: Windows XP/Vista/7 * Other Software REQUIRED: Intel Visual Fortran 10.x XE2013

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Cite this (Advanced Neuroscience Imaging Research Laboratory Software Packages, RRID:SCR_002926)

URL: http://www.fmri.wfubmc.edu/cms/software

Resource Type: Resource, software resource, software toolkit

Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime.

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    affydata

Cite this (affydata, RRID:SCR_016976)

URL: http://bioconductor.org/packages/release/data/experiment/html/affydata.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software, data or information resource

Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.

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    affy

Cite this (affy, RRID:SCR_012835)

URL: http://www.bioconductor.org/packages/release/bioc/html/affy.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.

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Cite this (Agilent G2565CA Microarray Scanner, RRID:SCR_017206)

URL: https://www.chem-agilent.com/contents.php?id=1000947

Resource Type: Resource, material resource

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.

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Cite this (Agilent Masshunter Qualitative Analysis, RRID:SCR_016657)

URL: https://www.agilent.com/en/products/software-informatics/masshunter-suite/masshunter-qualitative-analysis-gcms

Resource Type: Resource, data analysis software, data processing software, software application, data analytics software, software toolkit, software resource, data acquisition software

Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise.

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Cite this (Agile Protein Interactomes DataServer, RRID:SCR_008871)

URL: http://apid.dep.usal.es

Resource Type: Resource, data analysis service, data access protocol, database, analysis service resource, production service resource, web service, service resource, software resource, data or information resource

APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.

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Cite this (Alacris Theranostics, RRID:SCR_003953)

URL: http://www.alacris.de/

Resource Type: Resource, portal, organization portal, service resource, commercial organization, data or information resource

Commercial organization that uses next generation sequencing technologies coupled with computational modeling of tumor and somatic tissues in order to identify individualized therapies for cancer patients. The company also uses these technologies to help pharmaceutical partners stratify patients for their clinical trials. Alacris has an exclusive worldwide commercial license for the computational modeling of tumors and somatic tissues using proprietary computational systems modeling technologies ModCell developed at the Max Planck Institute for Molecular Genetics (MPI-MG) in Berlin coupled with next generation sequencing and genotyping technology developed at Harvard Medical School in Boston. The company also is building up the first next generation sequencing center in Europe for clinical operations.

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    ALEA

Cite this (ALEA, RRID:SCR_006417)

URL: http://www.bcgsc.ca/platform/bioinfo/software/alea

Resource Type: Resource, software resource, software toolkit

A computational software toolbox for allele-specific (AS) epigenomics analysis. It incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. It provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project) to reconstruct diploid in-silico genomes for human or hybrid mice under study. Then, for each accompanying ChIP-seq or RNA-seq dataset, it generates two Wiggle track format (WIG) files from short reads aligned differentially to each haplotype.

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Cite this (AltAnalyze - Alternative Splicing Analysis Tool, RRID:SCR_002951)

URL: http://www.altanalyze.org/

Resource Type: Resource, software resource, software application

Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.

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    ALTER

Cite this (ALTER, RRID:SCR_015968)

URL: http://sing.ei.uvigo.es/ALTER/

Resource Type: Resource, image analysis software, data analysis software, data processing software, alignment software, software application, sequence analysis software, web application, software resource

Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats.

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    Althia

Cite this (Althia, RRID:SCR_003918)

URL: http://www.althia.es/

Resource Type: Resource, portal, organization portal, service resource, commercial organization, data or information resource

A biomedical company in Spain focused on the development of new tools for diagnosis and personalized treatment of oncological diseases and precancerous. It has three areas of activity in permanent innovation: Assistance in Diagnosis / Prognosis in solid and hematological tumors, Translational Research covering the gap between basic and clinical research and advanced radiotherapy treatments based image-guided single dose (SD-IGRT). Their objectives are: * Provide an integrated tissue and tumor molecular phenotype analysis using the most advanced technologies in diagnosis, to guide the most appropriate treatment for each patient. * Discover and validate molecular patterns by molecular systems and platforms including pathology, to generate predictive algorithms through computational biology, evolution and determining the response of patients with a particular tumor profile. Althia has laboratories equipped with the most advanced equipment and technologies in Barcelona and Granada Genyo Center, with offices in Madrid.

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Cite this (Ancient conserved untranslated sequences, RRID:SCR_008130)

URL: http://pbil.univ-lyon1.fr/acuts/ACUTS.html

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Database that identifies new regulatory elements in untranslated regions of protein-coding genes (5 prime flanks, 5 prime UTRs, introns, 3 prime UTRs and 3 prime flanks). The analyses is focused on genes from metazoan species (essentially vertebrates, insects and nematodes). Information on highly conserved regions (sequences, alignments, annotations, bibliographic references) are compiled. Currently 176 out of 326 detected highly conserved regions (HCRs) have been analyzed and incorporated in the database. You can also access the list of annotated conserved elements and the list of conserved elements that remain to be processed. Their approach is based on comparative sequence analysis, for the identification of phylogenetic footprints.

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    andi

Cite this (andi, RRID:SCR_015971)

URL: https://github.com/EvolBioInf/andi

Resource Type: Resource, image analysis software, data processing software, alignment software, software application, algorithm resource, software resource

Algorithm for rapidly computing and estimating the evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.

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Cite this (AnimalTracker, RRID:SCR_014397)

URL: http://animaltracker.elte.hu/

Resource Type: Resource, software resource, software application, data analysis software, data processing software

A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation.

  • From Current Category

    Anima

Cite this (Anima, RRID:SCR_017017)

URL: https://github.com/Inria-Visages/Anima-Public/wiki

Resource Type: Resource, image analysis software, mri 3d image, data analysis software, data processing software, software application, 3d spatial image, diffusion-weighted mri 3d image, software resource, software toolkit, image processing software, registration software, image, data or information resource

Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS (OSX, Fedora, Ubuntu, Windows).

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Cite this (Anima scripts, RRID:SCR_017072)

URL: https://github.com/Inria-Visages/Anima-Scripts-Public/wiki

Resource Type: Resource, software resource, software application, image processing software, data processing software

Open source scripts for medical image processing. Provides set of scripts in Python shell.

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