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http://www.bioconductor.org/packages/release/bioc/html/MiChip.html

Software package that takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.

Proper citation: MiChip (RRID:SCR_001341) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/frma.html

Preprocessing and analysis software for single microarrays and microarray batches.

Proper citation: fRMA (RRID:SCR_001345) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/arrayQualityMetrics.html

Software package that generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). Reports contain both general and platform-specific sections. Both one and two color array platforms are supported.

Proper citation: arrayQualityMetrics (RRID:SCR_001335) Copy   

•   Source: SciCrunch Registry

https://rdrr.io/bioc/DEDS/

Software library that contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements methodology (Differential Expression via Distance Summary) which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.

Proper citation: DEDS (RRID:SCR_001339) Copy   

•   Source: SciCrunch Registry

http://sfld.rbvi.ucsf.edu/

A database of hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities. The SFLD classifies evolutionarily related enzymes according to shared chemical functions and maps these shared functions to conserved active site features. The classification is hierarchical, where broader levels encompass more distantly related proteins with fewer shared features. It thus serves as the analysis and archive site for superfamilies targeted by the Enzyme Function Initiative, and is developed by the Babbitt Laboratory in collaboration with the UCSF Resource for Biocomputing, Visualization, and Informatics. The resource also provides a collection of tools and data for investigating sequence-structure-function relationships and hypothesizing function.

Proper citation: Structure-function linkage database (RRID:SCR_001375) Copy   

•   Source: SciCrunch Registry

https://www.ddbj.nig.ac.jp/dra/index-e.html

Archive database for output data generated by next-generation sequencing machines including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, and others. DRA is a member of the International Nucleotide Sequence Database Collaboration (INSDC) and archiving the data in a close collaboration with NCBI Sequence Read Archive (SRA) and EBI Sequence Read Archive (ERA). Please submit the trace data from conventional capillary sequencers to DDBJ Trace Archive., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DDBJ Sequence Read Archive (RRID:SCR_001370) Copy   

•   Source: SciCrunch Registry

http://igb.agri.gov.il/main/index.pl

Biobank which collects, preserves, and assesses gene information related to species of plants indigenous to Israel. The Bank's goal is to conserve representative gene pools of species whose economic potential has yet to be developed.

Proper citation: Israel Plant Gene Bank (RRID:SCR_001403) Copy   

•   Source: SciCrunch Registry

http://www.usc.edu/dept/biomed/UTRC/

Biomedical technology research center focusing on the development of very high frequency (above 20 MHz) ultrasonic transducers/arrays for applications in medicine and biology that include ophthalmology, dermatology, vascular surgery, and small animal imaging. The research is pursued simultaneously in three directions: novel piezoelectric materials, very high frequency single element transducers and linear arrays, and finite element modeling and material property measurements. The Center also serves the community through collaborative efforts with investigators having a research interest in high-frequency ultrasound imaging. In addition, it performs the function of training and information dissemination by offering conferences, seminars and specialized courses at the University of Southern California. The Center has set forth a number of goals which define its mission: * Conduct novel research and development of very high frequency (>20MHz) ultrasonic transducers, arrays and imaging applications * Collaborate with other academic institutions, non-profit organizations, and small businesses supported by the NIH to further the development of these high-frequency applications and provide the expertise in transducers necessary for project success * Serve as an educational center for training scientists and engineers interested in ultrasonic transducer technology One of the primary goals of the Center is to provide service to outside investigators and small business. Often an investigator or company has a specific application in mind but is without the expertise to develop the necessary ultrasonic device. Investigators at academic institutions, research institutes, or small businesses supported by NIH grants who have a need for medical ultrasound transducers and are interested in a collaborative effort should contact Dr. Hyung Ham Kim or Dr. K. Kirk Shung. Ultrasound transducers and components can be fabricated either completely by center personnel or in a joint effort with other investigators. In addition, collaborators are encouraged to visit the facility for additional training in fabrication and assembly.

Proper citation: Resource Center for Medical Ultrasonic Transducer Technology (RRID:SCR_001404) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages//2.13/bioc/html/virtualArray.html

Software package that permits the user to combine raw data of different microarray platforms into one virtual array. It consists of several functions that act subsequently in a semi-automatic way. Doing as much of the data combination and letting the user concentrate on analyzing the resulting virtual array.

Proper citation: virtualArray (RRID:SCR_001361) Copy   

•   Source: SciCrunch Registry

http://www.jaduniv.edu.in/

Public state university in West Bengal, India. There is a focus on interdisciplinary learning and research; the university features a variety of centers such as school of education technology, cognitive sciences, and natural product studies.

Proper citation: Jadavpur University; West Bengal; India (RRID:SCR_001366) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/rama.html

Software package for robust estimation of cDNA microarray intensities with replicates. It uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance.

Proper citation: RAMA (RRID:SCR_001358) Copy   

•   Source: SciCrunch Registry

https://bioportal.bioontology.org/ontologies/NCBI_NMOsp_1_2_2

NeuroMorpho.Org light species ontology is a customized taxonomy for species available in NeuroMorpho.Org. This file is created from the existing resources like NCBI Taxonomy, NIF organism, Rat strain ontology, and Jax mice catalogue. The OBO file can be explored and downloaded from the NCBO bioportal service. The current NCBI_NMOsp_v1.2.2.obo file consists of 887 concepts of which 24 unique classes are mapped onto species & strains data in NeuroMorpho.Org database.

Proper citation: NeuroMorpho.Org light species ontology (RRID:SCR_001394) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/MANOR.html

Software packqge for importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH (Comparative genomic hybridization) experiments.

Proper citation: MANOR (RRID:SCR_001305) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/limmaGUI.html

Software package for a Graphical User Interface for the limma Microarray package.

Proper citation: limmaGUI (RRID:SCR_001306) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ffpe.html

Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

Proper citation: ffpe (RRID:SCR_001307) Copy   

•   Source: SciCrunch Registry

http://neuralensemble.org/

Community-based initiative to promote and co-ordinate open-source software development in neuroscience hosting a number of software projects for computational and systems neuroscience, including PyNN, NeuroTools, Brian, Neo, OpenElectrophy, libNeuroML and Sumatra. Some of the projects use their Trac installation, others are on GitHub. By grouping these projects together under the NeuralEnsemble umbrella, the aim is to maximize interoperability and build components that can easily be combined into powerful systems for brain simulations and advanced data analysis. An annual CodeJam workshop is organized, bringing together scientists, graduate students, and scientific programmers to share ideas, present their work, and write code together. These workshops have been hugely effective in catalyzing open-source neuroscience software development. There is a NeuralEnsemble Google group for discussion of collaborative neuroscience software development (mainly in Python, but users of other languages are welcome!) and to provide software support.

Proper citation: NeuralEnsemble (RRID:SCR_001382) Copy   

•   Source: SciCrunch Registry

http://clarityresourcecenter.org/

Protocols and other training materials related to the CLARITY protocol, a technique for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable.

Proper citation: Clarity resources (RRID:SCR_001387) Copy   

•   Source: SciCrunch Registry

http://www.qiqqa.com/

Qiqqa is a free reference management tool that provides all the tools you need to manage your documents and notes effectively, visualize your ideas, and find insights you would have missed otherwise. Engineered by academics, its mission is to make your research life easier. Qiqqa allows users to annotate PDF''s, assign tags, share documents and offers cloud storage for a nominal fee. We help academics, researchers, and professionals manage all their PDFs and get more out of them, with our award winning Qiqqa software. * PDF management, OCR, reading, annotation * Unique tools to understand and discover * Cloud sync, cite, and much much more * Free. Trusted by academia and industry for all five stages of the knowledge lifecycle. Add all your papers, and it helps you do all the rest, quicker. # Organize # Discover # Review and Understand # Collaborate # Create

Proper citation: qiqqa (RRID:SCR_004440) Copy   

•   Source: SciCrunch Registry

https://nda.nih.gov/

The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. Research data repository for data sharing and collaboration among investigators. Used to accelerate scientific discovery through data sharing across all of mental health and other research communities, data harmonization and reporting of research results. Infrastructure created by National Database for Autism Research (NDAR), Research Domain Criteria Database (RDoCdb), National Database for Clinical Trials related to Mental Illness (NDCT), and NIH Pediatric MRI Repository (PedsMRI).

Proper citation: NIMH Data Archive (RRID:SCR_004434) Copy   

•   Source: SciCrunch Registry

http://www.origene.com.cn/

A commercial antibody vendor.

Proper citation: Origene China (RRID:SCR_004436) Copy   

•   Source: SciCrunch Registry