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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ProteinPilot Resource Report Resource Website 100+ mentions |
ProteinPilot (RRID:SCR_024414) | data analysis software, software resource, data processing software, software application | Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems. | protein identification, protein expression analysis, post translational modification search, | is listed by: SoftCite | Restricted | https://sciex.com/content/dam/SCIEX/pdf/posters/ProteinPilot-Software-Overview.pdf | SCR_024414 | 2026-02-14 02:05:06 | 228 | |||||||||
|
pRRophetic Resource Report Resource Website 10+ mentions |
pRRophetic (RRID:SCR_024417) | software resource, simulation software, software application | Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data, | clinical chemotherapeutic response prediction, tumor gene expression levels, predict phenotypes, | is listed by: SoftCite | U01GM61393 ; GM089941 ; CA139278 ; University of Chicago ; UL1RR024999 |
PMID:25229481 | Free, Available for download, Freely available | SCR_024417 | 2026-02-14 02:05:18 | 23 | ||||||||
|
OMNISEC Resource Report Resource Website 10+ mentions |
OMNISEC (RRID:SCR_024485) | data analysis software, software resource, data processing software, software application | Software for OMNISEC instrument control, data acquisition, analysis and reporting. Used for advanced analysis of proteins and polymers by GPC/SEC, and is specifically designed for control of OMNISEC RESOLVE and OMNISEC REVEAL. | OMNISEC instrument control, data acquisition, analysis and reporting, proteins and polymers analysis, | is listed by: SoftCite | Restricted | SCR_024485 | 2026-02-14 02:05:19 | 38 | ||||||||||
|
PHYLDOG Resource Report Resource Website 1+ mentions |
PHYLDOG (RRID:SCR_024487) | data analysis software, software resource, data processing software, software application | Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously. | probabilistic model, reconstruct species tree and all corresponding gene trees, build gene and species trees, gene families analysis, genomes analysis simultaneously, gene families duplications and losses, | is listed by: SoftCite | PMID:23132911 | Free, Freely available | SCR_024487 | 2026-02-14 02:04:56 | 1 | |||||||||
|
ASTRAL-Pro Resource Report Resource Website 1+ mentions |
ASTRAL-Pro (RRID:SCR_024520) | software resource, simulation software, software application | Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy. | species tree reconstruction, reconstruction from multi-copy gene family trees | is listed by: SoftCite | PMID:32886770 | Free, Available for download, Freely available | SCR_024520 | ASTRAL for PaRalogs and Orthologs, ASTRAL-Pro 2 | 2026-02-14 02:05:15 | 3 | ||||||||
|
Kaplan Meier Plotter Resource Report Resource Website 1+ mentions |
Kaplan Meier Plotter (RRID:SCR_024521) | data access protocol, software resource, web service | Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma. | survival analysis, assess correlation between expression of genes and survival, tumor samples, | is listed by: SoftCite | PMID:34309564 | Free, Freely available | http://kmplot.com/analysis/index.php?p=service&cancer=custom_plot | SCR_024521 | Kaplan-Meier Plotter, KM Plotter | 2026-02-14 02:05:08 | 4 | |||||||
|
ProgRes Capture Pro Resource Report Resource Website 10+ mentions |
ProgRes Capture Pro (RRID:SCR_024489) | software resource, data processing software, data acquisition software, software application | Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras. | image acquisition, Jenoptik ProgRes microscope cameras, Jenoptik, | is listed by: SoftCite | PMID:34520656 | Free, Available for download, Freely available | SCR_024489 | Jenoptic ProgRes Capture Pro | 2026-02-14 02:05:07 | 12 | ||||||||
|
MADOKA Resource Report Resource Website 1+ mentions |
MADOKA (RRID:SCR_024522) | data access protocol, software resource, web service | Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library. | large scale protein structure similarity searching, searching similar protein structures, aligning input structure with whole PDB library, | is listed by: SoftCite | PMID:31870277 | Free, Freely available | SCR_024522 | 2026-02-14 02:05:19 | 1 | |||||||||
|
SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software resource, software toolkit | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-02-14 02:04:59 | 101 | |||
|
jcvi Resource Report Resource Website 10+ mentions |
jcvi (RRID:SCR_021641) | software resource, software library, software toolkit | Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. | Python libraries, parse bioinformatics files, assembly, annotation, comparative genomics | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/tanghaibao/jcvi/tree/v0.5.7 https://zenodo.org/record/31631#.YRaieYhKhPa |
SCR_021641 | jcvi_PyPI, jcvi 1.1.17 | 2026-02-14 02:04:46 | 15 | ||||||||
|
CalcuSyn Resource Report Resource Website 50+ mentions |
CalcuSyn (RRID:SCR_020251) | data analysis software, software resource, data processing software, software application | Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools. | Biosoft, drug mixtures study, drug efficacy, dose effect, quantify synergism, quantify inhibition | is listed by: SoftCite | Restricted | SCR_020251 | CalcuSyn Version 2.0 | 2026-02-14 02:04:20 | 57 | |||||||||
|
NONMEM Resource Report Resource Website 10+ mentions |
NONMEM (RRID:SCR_016986) | Nonmem | data processing software, data analysis software, software application, software resource, simulation software | Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions. | nonlinear, mixed, effect, modeling, pharmacokinetic, pharmacodynamic, analysis, data | is listed by: SoftCite | Commercially available | SCR_016986 | NONMEM 7.4, NONMEM 7, Nonlinear mixed effects modelling software, NONMEM 7.2, NONlinear Mixed Effects Modeling software, population analysis | 2026-02-14 02:04:34 | 42 | ||||||||
|
SignalP Resource Report Resource Website 5000+ mentions |
SignalP (RRID:SCR_015644) | software resource, web application | Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. | prediction, signal peptide, cleavage site, amino acid, sequence, artificial neural network |
is listed by: SoftCite has parent organization: DTU Center for Biological Sequence Analysis |
PMID:28451972 | Freely available, Acknowledgment requested, Free, Available for download, Runs on Windows, Runs on Mac OS | SCR_015644 | 2026-02-14 02:04:43 | 9406 | |||||||||
|
MRIcron Resource Report Resource Website 1000+ mentions |
MRIcron (RRID:SCR_002403) | MRIcron | data visualization software, software resource, data processing software, software application | Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. | NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools |
is used by: XFSL: An FSL toolbox is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: neurodebian is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Colour maps for brain imaging has parent organization: University of South Carolina; South Carolina; USA |
PMID:17583985 PMID:11568431 |
BSD License | biotools:MRIcron, nif-0000-00122 | https://sources.debian.org/src/mricron/ http://www.mccauslandcenter.sc.edu/mricro/ http://www.nitrc.org/projects/mricron http://neuro.debian.net/pkgs/mricron.html https://bio.tools/MRIcron |
SCR_002403 | mricron - magnetic resonance image conversion viewing and analysis | 2026-02-14 02:05:07 | 2194 | |||||
|
QuantPrime Resource Report Resource Website 100+ mentions |
QuantPrime (RRID:SCR_015498) | software resource, web application | Fully automated tool for primer pair design in small- to large-scale real-time reverse transcription qPCR analyses. It offers design and specificity checking with highly customizable parameters and is available for use with publicly available eukaryotic transcriptomes. | primer design, primer pair design, rt-qpcr, reverse transcription qpcr | is listed by: SoftCite | DOI:10.1186/1471-2105-9-465 | Acknowledgement requested, Available as a web application, Available as a desktop application | SCR_015498 | 2026-02-14 02:04:46 | 155 | |||||||||
|
ModFit LT Resource Report Resource Website 100+ mentions |
ModFit LT (RRID:SCR_016106) | data visualization software, software resource, data processing software, software application | Modeling software for flow cytometry histograms. Models for cell-tracking dye studies and synchronized cell lines are built right into the software. | flow, cytometry, histogram, model, graph, cell, tracking, dye, cell line | is listed by: SoftCite | Commercially available, Available for purchase, Trial available | SCR_016106 | Verity Software House ModFit LT | 2026-02-14 02:04:46 | 143 | |||||||||
|
Flowlogic Resource Report Resource Website 50+ mentions |
Flowlogic (RRID:SCR_020942) | data analysis software, software resource, data processing software, software application | Software tool for flow cytometry data analysis by Miltenyi Biotec. | Flow cytometry data, data analysis, flow cytometry, Miltenyi Biotec | is listed by: SoftCite | Restricted | SCR_020942 | Flowlogic TM Software, Flowlogic Software | 2026-02-14 02:04:41 | 74 | |||||||||
|
GRADEpro Resource Report Resource Website 100+ mentions |
GRADEpro (RRID:SCR_021308) | data management software, software resource, software application | Software tool used to create summary of findings tables for cochrane systematic reviews. Web application to create, manage and share summaries of research evidence called Evidence Profiles and Summary of Findings Tables. | Summary of findings tables, cochrane systematic reviews, research evidence creating, research evidence management, research evidence sharing summaries, evidence profiles, | is listed by: SoftCite | Restricted | https://cebgrade.mcmaster.ca/gradepro.html | SCR_021308 | Guideline Development Tool, GRADEpro GDT, GDT, GRADE Guideline Development Tool, G2DT | 2026-02-14 02:04:43 | 376 | ||||||||
|
ClustalW Resource Report Resource Website 10000+ mentions |
ClustalW (RRID:SCR_017277) | ClustalW of DDBJ | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.Web sevice of ClustalW provided by DNA data bank of Japan. | alignment, service, DNA, data, bank, Japan | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017277 | ClustalW of DNA Data Bank of Japan | 2026-02-14 02:03:23 | 10543 | ||||||||
|
EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | image processing software, software resource, data processing software, software application | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | EMAN1, EMAN2 | 2026-02-14 02:03:20 | 106 |
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:
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 facets that you can filter the data by.
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.
