Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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://github.com/ABCD-STUDY/geocoding
Software that uses a geo-location database to determine individuals' residential environment in Adolescent Brain Cognitive Development (ABCD) study. It performs queries given individuals' residential history in longitude and latitude.
Proper citation: geocoding (RRID:SCR_016007) Copy
http://bioconductor.org/packages/release/bioc/html/SC3.html
Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients.
Proper citation: SC3 (RRID:SCR_015953) Copy
https://github.com/haotianteng/Chiron
Software basecaller for Oxford Nanopore Technologies' sequencers.
Proper citation: Chiron (RRID:SCR_015950) Copy
http://www.hermit-reasoner.com/
Algorithm for a reasoner for ontologies written using the Web Ontology Language (OWL). Given an OWL file, HermiT can determine whether or not the ontology is consistent, identify subsumption relationships between classes, and much more.
Proper citation: HermiT OWL Reasoner (RRID:SCR_016006) Copy
https://github.com/osallou/cassiopee-c
Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity.
Proper citation: Cassiopee (RRID:SCR_016056) Copy
http://cdbfasta.sourceforge.net/
Software tool for indexing and retrieval of nucleotide sequences from FASTA (DNA and protein sequence alignment software) record databases. It has the option to compress data records.
Proper citation: Cdbfasta (RRID:SCR_016057) Copy
https://github.com/neurodroid/stimfit
Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy.
Proper citation: Stimfit (RRID:SCR_016050) Copy
http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Bio++ (RRID:SCR_016055) Copy
http://baderlab.org/Software/EnrichmentMap
Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together.
Proper citation: EnrichmentMap (RRID:SCR_016052) Copy
https://github.com/thegenemyers/DAZZ_DB
Software library and database to manage nucleotide sequencing read data. It stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files and avoid duplicating data.
Proper citation: Dazzler (RRID:SCR_016069) Copy
Software application to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation. The application accepts phylogenies in Newick format and can return the sequence of any node, allowing for the exact evolutionary history to be recorded at the discretion of users.
Proper citation: Dawg (RRID:SCR_016068) Copy
http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.
Proper citation: Clonalframe (RRID:SCR_016060) Copy
https://dazzlerblog.wordpress.com
Software alignment tool to find all significant local alignments between long and noisy, up to 15% on average reads encoded in a Dazzler database. Used for DNA sequence assembly, specifically for next generation long-read sequencers such as the Pacbio RS II and Sequel sequencers.
Proper citation: Daligner (RRID:SCR_016066) Copy
An Antibody supplier
Proper citation: B-Bridge International (RRID:SCR_013559) Copy
An Antibody supplier
Proper citation: Aviva Systems Biology (RRID:SCR_013560) Copy
An Antibody supplier
Proper citation: Astra Biotech GmbH (RRID:SCR_013564) Copy
http://www.gelifesciences.com/webapp/wcs/stores/servlet/catalog/en/GELifeSciences/brands/amersham/
An Antibody supplier
Proper citation: Amersham Biosciences (RRID:SCR_013566) Copy
http://www.idoimaging.com/program/160
A tool for visualization of structural and functional MRI volumes. Features include structural and functional overlay display of volume sections, volume annotation, ROI analysis, interfacing with FSL''s brain extraction, and 3D rendering. mri3dX should run on most unix workstations, but requires Motif and OpenGL/Mesa graphics libraries.
Proper citation: mri3dX (RRID:SCR_013609) Copy
An Antibody supplier
Proper citation: Alpha Diagnostic International (RRID:SCR_013568) Copy
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the T1D Resources search. From here you can search through a compilation of resources used by T1D and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that T1D has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on T1D then you can log in from here to get additional features in T1D such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into T1D you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within T1D that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
