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/PathwayAnalysisPlatform/PathwayMatcher
Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome.
Proper citation: PathwayMatcher (RRID:SCR_016759) Copy
http://emg.nysbc.org/redmine/projects/leginon/wiki/Leginon_Homepage
System designed for automated collection of images from a transmission electron microscope.
Proper citation: Leginon (RRID:SCR_016731) Copy
https://www.proteinmetrics.com/products/byonic/
Software package for advanced peptide and protein identification by tandem mass spectrometry. Allows to define unlimited number of variable modification type and allows the user to set a separate limit on the number of occurrences of each modification type.
Proper citation: PMI-Byonic (RRID:SCR_016735) Copy
https://github.com/hakyimlab/PrediXcan
Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype.
Proper citation: PrediXcan (RRID:SCR_016739) Copy
https://github.com/OpenSMFS/FRETBursts
Software for burst analysis of freely diffusing single-molecule Förster Resonance Energy Transfer (smFRET) experiments to study cellular processes at the molecular scale. Used for single and multi-spot single-molecule FRET (smFRET) data.
Proper citation: FRETBursts (RRID:SCR_016898) Copy
https://github.com/gelles-brandeis/CoSMoS_Analysis
Software tools for analyzing co-localization single-molecule spectroscopy image data.
Proper citation: CoSMoS_Analysis (RRID:SCR_016896) Copy
http://prosightlite.northwestern.edu/
Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data.
Proper citation: ProSight Lite (RRID:SCR_016908) Copy
http://nrtdp.northwestern.edu/
Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists.
Proper citation: National Resource for Translational and Developmental Proteomics (RRID:SCR_016907) Copy
Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.
Proper citation: MARRVEL (RRID:SCR_016871) Copy
https://www.sciencescott.com/pyminer
Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq.
Proper citation: PyMINEr (RRID:SCR_016990) Copy
https://github.com/yarden/MISO/blob/fastmiso/docs/source/sashimi.rst
Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions.
Proper citation: Sashimiplot (RRID:SCR_016861) Copy
https://github.com/fmaguire/Bridger_Assembler
Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.
Proper citation: Bridger (RRID:SCR_017039) Copy
https://panoramaweb.org/project/home/begin.view?
Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents.
Proper citation: PanoramaWeb (RRID:SCR_017136) Copy
http://pathwaynet.princeton.edu/
Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.
Proper citation: PathwayNet (RRID:SCR_017353) Copy
https://modbase.compbio.ucsf.edu/foxs/
Web server for computing theoretical scattering profile of structure and fitting of experimental profile. Computes SAXS profile of given atomistic model and fits it to experimental profile. Used for structural modeling applications with small angle X-ray scattering data.
Proper citation: FoXS (RRID:SCR_017269) Copy
Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager.
Proper citation: BEAST2 (RRID:SCR_017307) Copy
https://amp.pharm.mssm.edu/geneshot/
Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations.
Proper citation: Geneshot (RRID:SCR_017582) Copy
http://neuroproteomics.scs.illinois.edu/microMS.htm
Software Python platform for image guided Mass Spectrometry profiling. Provides graphical user interface for automatic cell finding and point based registration from whole slide images. Simplifies single cell analysis with feature rich image processing.
Proper citation: microMS (RRID:SCR_017443) Copy
Repository of biochemical, genetic, and structural information about DNA Polymerases. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software.
Proper citation: Polbase (RRID:SCR_006107) Copy
https://phenome.jax.org/centers/QTLA
Raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data. These data are provided as a courtesy to the genetic mapping community and may be used for purposes of developing or testing new analysis methods or software and for meta-analysis of quantitative traits. The authors of the datasets retain individual ownership of the data. As a courtesy to the authors, please alert them in advance of any publications that result from reanalysis of these data or obtain permission prior to redistribution of data or results. In all data sets and files, the marker locations have been translated to Cox build 37 coordinates unless otherwise stated. Please consider contributing your data to the QTL Archive.
Proper citation: QTL Archive (RRID:SCR_006213) 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.
