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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ROCit Resource Report Resource Website 1+ mentions |
ROCit (RRID:SCR_024420) | software toolkit, software resource | Software R package for assessing overall diagnostic ability of binary classifier. Used to evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot. | assessing overall diagnostic ability of binary classifier, evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024420 | Receiver Operating Characteristic it | 2026-02-15 09:22:42 | 1 | |||||||||
|
Rgdal Resource Report Resource Website 1+ mentions |
Rgdal (RRID:SCR_024422) | software toolkit, software resource | Software R package provides bindings for the Geospatial Data Abstraction Library. Translator library for raster and vector geospatial data formats. | Translator library, geospatial data formats, Geospatial Data Abstraction Library bindings, | is listed by: SoftCite | Free, Available for download, Freely available | https://r-forge.r-project.org/projects/rgdal/ | SCR_024422 | , R geospatial data abstraction library, rgdal | 2026-02-15 09:23:29 | 3 | ||||||||
|
survivalROC Resource Report Resource Website 1+ mentions |
survivalROC (RRID:SCR_024415) | software toolkit, software resource | Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data. | compute time dependent Receiver Operating Characteristic curve, censored survival data, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024415 | survival Receiver Operating Characteristic | 2026-02-15 09:22:42 | 9 | |||||||||
|
ggridges Resource Report Resource Website 1+ mentions |
ggridges (RRID:SCR_024511) | software toolkit, software resource | Software R package enables creation of Ridgeline plots in 'ggplot2' | creation of Ridgeline plots in 'ggplot2', | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/wilkelab/ggridges | SCR_024511 | 2026-02-15 09:23:34 | 5 | |||||||||
|
gamm4 Resource Report Resource Website 1+ mentions |
gamm4 (RRID:SCR_024507) | software toolkit, software resource | Software R package to estimate generalized additive mixed models. | estimate generalized additive mixed models, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024507 | 2026-02-15 09:23:33 | 3 | ||||||||||
|
Optimization Toolbox Resource Report Resource Website 1+ mentions |
Optimization Toolbox (RRID:SCR_024486) | software toolkit, software resource | Software package provides functions for finding parameters that minimize or maximize objectives while satisfying constraints. Toolbox includes solvers for linear programming, mixed integer linear programming, quadratic programming, second order cone programming, nonlinear programming, constrained linear least squares, nonlinear least squares, nonlinear equations. | Mathworks, finding parameters, minimize or maximize objectives, linear programming solver, mixed integer linear programming solver, quadratic programming solver, second order cone programming solver, nonlinear programming solver, constrained linear least squares solver, nonlinear least squares solver, nonlinear equations solver, | is listed by: SoftCite | Restricted | SCR_024486 | 2026-02-15 09:22:43 | 1 | ||||||||||
|
CopyKAT Resource Report Resource Website 50+ mentions |
CopyKAT (RRID:SCR_024512) | software toolkit, software resource | Software R package to estimate genomic copy number profiles at average genomic resolution of 5 Mb from read depth in high throughput single cell RNA sequencing data.Used for inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data. | Inference of genomic copy number and subclonal structure of human tumors, high throughput single cell RNAseq data, | is listed by: SoftCite | PMID:33462507 | Free, Available for download, Freely available | SCR_024512 | , Copynumber Karyotyping of Aneuploid Tumors | 2026-02-15 09:23:31 | 65 | ||||||||
|
classInt Resource Report Resource Website 1+ mentions |
classInt (RRID:SCR_024515) | software toolkit, software resource | Software R package for choosing univariate class intervals for mapping or other graphics purposes. | choosing univariate class intervals, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/r-spatial/classInt/ | SCR_024515 | Class Intervals | 2026-02-15 09:23:34 | 2 | ||||||||
|
mitml Resource Report Resource Website 1+ mentions |
mitml (RRID:SCR_024516) | software toolkit, software resource | Software R package for multiple imputation of missing data in multilevel modeling. | multiple imputation of missing data in multilevel modeling, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/simongrund1/mitml | SCR_024516 | 2026-02-15 09:23:31 | 1 | |||||||||
|
GenePattern Resource Report Resource Website 1000+ mentions |
GenePattern (RRID:SCR_003201) | GenePattern | software application, data processing software, data analysis software, software resource | A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. | gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is affiliated with: GenePattern Notebook is related to: TIGRESS has parent organization: Broad Institute |
NCI ; NIGMS |
PMID:16642009 | Free, Freely available | biotools:genepattern, OMICS_01855, nif-0000-30654 | https://bio.tools/genepattern | SCR_003201 | 2026-02-15 09:18:28 | 1078 | |||||
|
geNORM Resource Report Resource Website 5000+ mentions |
geNORM (RRID:SCR_006763) | GENORM | software application, data processing software, data analysis software, software resource | Software to determine most stable reference (housekeeping) genes from set of tested candidate reference genes in given sample panel. From this, gene expression normalization factor can be calculated for each sample based geometric mean of user-defined number of reference genes. | reference gene, quantitative real time pcr |
is used by: RefFinder is listed by: OMICtools is listed by: SoftCite is related to: qBasePLUS has parent organization: Ghent University; Ghent; Belgium |
PMID:19131113 PMID:12519963 |
nlx_156922, OMICS_02316 | http://medgen.ugent.be/~jvdesomp/genorm/ | SCR_006763 | 2026-02-15 09:19:34 | 5230 | |||||||
|
QIIME Resource Report Resource Website 10000+ mentions |
QIIME (RRID:SCR_008249) | software application, data processing software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics. | microbiome, microbial community, sequence data, data analysis software, bio.tools |
is used by: SortMeRNA is used by: Nephele is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Colorado Boulder; Colorado; USA |
DOI:10.1038/nmeth.f.303 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01118, SCR_011948, OMICS_01521, biotools:qiime | https://bio.tools/qiime | SCR_008249 | Quantitative Insights Into Microbial Ecology | 2026-02-15 09:19:44 | 11036 | ||||||
|
MACH Resource Report Resource Website 500+ mentions |
MACH (RRID:SCR_009621) | software application, data processing software, data analysis software, software resource | QTL analysis based on imputed dosages/posterior_probabilities. | genetic association, genomic analysis, imaging genomics, snp, gene, quantitative trait analysis, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 DOI:10.1002/gepi.20533 |
Free, Non-commercial, Acknowledgement requested | nlx_155856, biotools:mach | http://www.nitrc.org/projects/mach https://bio.tools/mach |
https://sources.debian.org/src/mach-haplotyper/ | SCR_009621 | mach2qtl, MaCH | 2026-02-15 09:20:13 | 925 | |||||
|
LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | software application, data processing software, data analysis software, software resource | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool https://bio.tools/limma https://sources.debian.org/src/r-bioc-limma/ |
SCR_010943 | Linear Models for Microarray Data | 2026-02-15 09:20:21 | 24583 | ||||||
|
CANGS Resource Report Resource Website 1+ mentions |
CANGS (RRID:SCR_011837) | CANGS | software application, data processing software, data analysis software, software resource | A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. | windows, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20180949 | biotools:cangs, OMICS_01084 | https://bio.tools/cangs | SCR_011837 | 2026-02-15 09:20:27 | 1 | |||||||
|
affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | software application, data processing software, data analysis software, software resource | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy https://sources.debian.org/src/r-bioc-affy/ |
SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-02-15 09:20:39 | 2996 | ||||
|
MolProbity Resource Report Resource Website 5000+ mentions |
MolProbity (RRID:SCR_014226) | web application, software resource | A structure-validation web application which provides an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. MolProbity works best as an active validation tool (used as soon as a model is available and during each rebuild/refine loop) and when used for protein and RNA crystal structures, but it may also work well for DNA, ligands and NMR ensembles. It produces coordinates, graphics, and numerical evaluations that integrate with either manual or automated use in systems such as PHENIX, KiNG, or Coot. | web application, consultation, macromolecular structure, structure validation, macromolecular crystallography |
is listed by: SoftCite is related to: Phenix is related to: Coot has parent organization: Duke University; North Carolina; USA |
Howard Hughes Medical Institute Predoctoral Fellowship ; NIGMS GM-15000; NIGMS GM-61302 |
DOI:10.1107/S0907444909042073 | Acknowledgement requested, Requires Java and Javascript | https://www.phenix-online.org/documentation/reference/molprobity_tool.html | SCR_014226 | 2026-02-15 09:20:53 | 6313 | |||||||
|
Minitab Resource Report Resource Website 5000+ mentions |
Minitab (RRID:SCR_014483) | software application, data processing software, data analysis software, software resource | A statistical software package that allows the user to import data, create graphs, and perform statistical analysis. It can perform basic statistical tests like descriptive statistics, hypothesis tests, confidence intervals, and normality tests as well as regression and ANOVA and quality assessment. | data analysis, statistical analysis, hypothesis, confidence, descriptive | is listed by: SoftCite | SCR_014483 | 2026-02-15 09:20:43 | 5778 | |||||||||||
|
I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | software application, data processing software, data analysis software, software resource | Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation. | Automated prediction, protein structure prediction, protein function prediction, protein 3D structure, amino acid sequence, alignment, simulation, 3D atomic model, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Kansas; Kansas; USA |
NIGMS GM083107; NIGMS GM084222 |
DOI:10.1186/1471-2105-9-40 DOI:10.1093/nar/gkv342 PMID:20360767 PMID:18215316 |
Free, Available for download, Freely available | biotools:i-tasser, SCR_018803 | https://bio.tools/i-tasser | SCR_014627 | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-02-15 09:21:06 | 3702 | |||||
|
CVODE Resource Report Resource Website 50+ mentions |
CVODE (RRID:SCR_014696) | software application, data processing software, data analysis software, software resource | Solver for stiff and nonstiff ordinary differential equation (ODE) systems (initial value problem), given in explicit form y' = f(t,y), based on Adams and BDF methods. It is one of the programs that makes up the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis software, solver, equation solver, ordinary differential equation, differential equation, stiff, nonstiff | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014696 | SUNDIALS CVODE | 2026-02-15 09:21:01 | 56 |
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 nidm-terms Resources search. From here you can search through a compilation of resources used by nidm-terms and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that nidm-terms 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 nidm-terms then you can log in from here to get additional features in nidm-terms 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 nidm-terms 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.
