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://www.bibliometrix.org/home/
Software R package for comprehensive science mapping analysis. Used for quantitative research in scientometrics and bibliometrics that includes all main bibliometric methods of analysis.
Proper citation: bibliometrix (RRID:SCR_023744) Copy
https://www.cubi.bihealth.org/software/varfish/
Web application for quality control, filtering, prioritization, analysis, and user based annotation of DNA variant data with focus on rare disease genetics. Comprehensive DNA variant analysis for diagnostics and research.
Proper citation: VarFish (RRID:SCR_023710) Copy
https://github.com/rrwick/Filtlong
Software tool for filtering long reads by quality.Can take set of long reads and produce smaller, better subset. Uses both read length and read identity when choosing which reads pass the filter.
Proper citation: Filtlong (RRID:SCR_024020) Copy
https://pypi.org/project/oncoboxlib/
Software library to calculate Pathways Activation Levels. It takes file that contains gene symbols in HGNC format, their expression levels for one or more samples and calculates PAL values for each pathway in each sample.
Proper citation: oncoboxlib (RRID:SCR_023722) Copy
https://github.com/Martinsos/edlib
Software C/C++ (and Python) library for sequence alignment using edit (Levenshtein) distance.
Proper citation: Edlib (RRID:SCR_024078) Copy
https://github.com/GATB/MindTheGap
Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome.
Proper citation: MindTheGap (RRID:SCR_024115) Copy
Web tool for predictive sgRNA-scoring that captures sequence features affecting Cas9/sgRNA activity in vivo. Scoring algorithm to help select the best gRNAs for CRISPR.
Proper citation: CRISPRscan (RRID:SCR_023777) Copy
Cancer research platform that aggregates clinical, genomic and functional data from various types of patient derived cancer models, xenographs, organoids and cell lines. Open catalog of harmonised patient-derived cancer models. Standardises, harmonises and integrates clinical metadata, molecular and treatment-based data from academic and commercial providers worldwide. Data is FAIR and underpins generation and testing of new hypotheses in cancer mechanisms and personalised medicine development. PDCM Finder have expanded to organoids and cell lines and is now called CancerModels.Org. PDCM Finder was launched in April 2022 as successor of PDX Finder portal, which focused solely on patient-derived xenograft models.
Proper citation: CancerModels.Org (RRID:SCR_023931) Copy
https://pmc.ncbi.nlm.nih.gov/articles/PMC4525701/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 25,2025. Web tool to parse Sanger sequencing chromatograms with double peaks into wildtype and alternative allele sequences. Used to separate chromatogram data containing ambiguous base calls into wildtype and mutant allele sequences.Used for identification of unknown indels using sanger sequencing of polymerase chain reaction products.
Proper citation: Poly Peak Parser (RRID:SCR_023776) Copy
https://jydu.github.io/maffilter/
Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc.
Proper citation: MafFilter (RRID:SCR_024105) Copy
https://sparta.readthedocs.io/en/latest/
Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms.
Proper citation: sparta (RRID:SCR_024349) Copy
https://github.com/Pas-Kapli/mptp
Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets.
Proper citation: mPTP (RRID:SCR_024121) Copy
http://ugovaretto.github.io/molekel/
Open source multi platform molecular visualization program.
Proper citation: Molekel (RRID:SCR_024122) Copy
Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.
Proper citation: MRtrix3 (RRID:SCR_024123) Copy
Software application for isothermal titration calorimetry performed on MicroCal PEAQ instrument by Malvern.
Proper citation: Malvern Panalytical MicroCal PEAQ-ITC analysis (RRID:SCR_023795) Copy
Software visualization tool for biological pathways. Pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. Developed in Java and can be extended with plugins.
Proper citation: PathVisio (RRID:SCR_023789) Copy
Regularly collects nationally representative data about American public’s knowledge of, attitudes toward, and use of cancer and health related information. HINTS data are used to monitor changes in fields of health communication and health information technology and to create more effective health communication strategies across different populations. Weighted, nationally representative probability based survey of civilian, non-institutionalized adults administered by National Cancer Institute on knowledge of and attitudes toward cancer relevant information.
Proper citation: Health Information National Trends Survey (RRID:SCR_023943) Copy
A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences.
Proper citation: cpnDB: A Chaperonin Database (RRID:SCR_002263) Copy
https://elucidata.io/el-maven/
Open source LC-MS data processing engine for simplifying metabolomics analysis. Mass spectrometry data processing engine that is optimal for isotopomer labeling and global metabolomic profiling experiments. Interactive software platform that accelerates analysis of LC-MS, GC-MS, and LC-MS/MS datasets.
Proper citation: EL MAVEN (RRID:SCR_022159) Copy
http://www.theseed.org/wiki/Home_of_the_SEED
The SEED is a framework to support comparative analysis and annotation of genomes. The cooperative effort focuses on the development of the comparative genomics environment and, more importantly, on the development of curated genomic data. Curation of genomic data (annotation) is done via the curation of subsystems by an expert annotator across many genomes, not on a gene by gene basis. From the curated subsystems we extract a set of freely available protein families (FIGfams). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free RAST-Server (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the Metagenomics-RAST-Server freely available. We also provide a SEED-Viewer that allows read-only access to the latest curated data sets. We currently have 58 Archaea, 902 Bacteria, 562 Eukaryota, 1254 Plasmids and 1713 Viruses in our database. All tools and datasets that make up the SEED are in the public domain and can be downloaded at ftp://ftp.theseed.org
Proper citation: SEED (RRID:SCR_002129) 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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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 RRID 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.
