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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
LRPath Resource Report Resource Website 1+ mentions |
LRPath (RRID:SCR_018572) | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data. | Gene, map, gene set, gene set testing, identifying enriched biologically group, gene expression data, gene expression, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIEHS P30 ES06096; NIEHS U01 ES015675; NHGRI R01 HG003749; NLM R01 LM008106; NIDA U54 DA021519 |
PMID:19038984 | Free, Freely available | biotools:lrpath | https://bio.tools/lrpath | SCR_018572 | 2026-02-14 02:03:39 | 4 | ||||||
|
ReproMan Resource Report Resource Website 1+ mentions |
ReproMan (RRID:SCR_018468) | data management software, software resource, software toolkit, software application | Software tool to simplify creation and management of computing environments in Neuroimaging. | Simplify computing environment creation, computing environment management, neuroimaging, imaging, data | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | ReproMan is under development. | https://github.com/ReproNim/reproman | SCR_018468 | 2026-02-14 02:03:35 | 1 | |||||||||
|
CurveFitter Resource Report Resource Website 1+ mentions |
CurveFitter (RRID:SCR_018461) | data analysis software, software resource, data processing software, software application | Software tool for growth curve fitting and visualization. Program allows to fit growth curve using simple GUI or advanced scripting environment. Used to fit growth curves generated for data collected in microtiter plates or elsewhere. | Growth curve fitting, data visualization, data, microtiter plate data, microbiology, microtiter plate | Free, Available for download, Freely available | https://archive.codeplex.com/?p=curvefitter | SCR_018461 | curvefitter | 2026-02-14 02:03:38 | 3 | |||||||||
|
Big Data Processor Resource Report Resource Website 1+ mentions |
Big Data Processor (RRID:SCR_018484) | BDP | data processing software, software application, image processing software, software resource, image analysis software | Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy. | Image, image processor, data processor, data, processing, analysis, image data, microscopy | is a plug in for: Fiji | Free, Available for download, Freely available | https://github.com/embl-cba/fiji-plugin-bigDataProcessor | SCR_018484 | 2026-02-14 02:03:33 | 2 | ||||||||
|
Islet eQTL Explorer Resource Report Resource Website 1+ mentions |
Islet eQTL Explorer (RRID:SCR_018692) | web service, data or information resource, service resource, data access protocol, software resource | Web tool for exploring variants in islet expression quantitative trait loci. Data is result of collaboration between Michigan University Parker lab, Department of Biostatistics and Center for Statistical Genetics at University of Michigan, National Human Genome Research Institute, Jackson Laboratory for Genomic Medicine, Department of Genetics at University of North Carolina, European Bioinformatics Institute, Department of Preventive Medicine at University of Southern California, and Department of Physiology and Biophysics at University of Southern California. | Exploring variants, islet expression, quantitative trait loci, data, chromatin, chromatin state annotation, gene, footprint, allele | has parent organization: University of Michigan; Ann Arbor; USA | Free, Freely available | SCR_018692 | 2026-02-14 02:03:38 | 1 | ||||||||||
|
Stanford Medicine Research Data Repository Resource Report Resource Website 100+ mentions |
Stanford Medicine Research Data Repository (RRID:SCR_018686) | STARR | data repository, storage service resource, service resource | Platform developed and operated by Stanford Medicine Research IT team for working with clinical data for research purposes. Permits collection and aggregation of all clinical data generated at Stanford for care purposes, and articulates formal approval process each research project must follow in order to obtain and work with this data for research purpose. Home of stride/web tools for Cohort Discovery and Chart Review. | Clinical data, Stanford data, care purpose, stride web tools, cohort discovery, data | is related to: Stanford University School of Medicine; California; USA | Restricted | https://starr.stanford.edu/team | SCR_018686 | STRIDE-web, STAnford medicine Research data Repository | 2026-02-14 02:03:39 | 213 | |||||||
|
Mutation and Patient Database Resource Report Resource Website 1+ mentions |
Mutation and Patient Database (RRID:SCR_018806) | data set, data or information resource, database | Collection of published mutations and sequence variations in genes that cause Neuronal Ceroid Lipofuscinoses together with unpublished data included with permission. There are two tables for each human NCL disease gene - Patient Datasheets list all published or reported patients and families, and Mutation Datasheets list all published or reported mutations, cross-referenced to patient table. Datasheets are available to view or download as excel files for off-site use to aid local needs or interests. Database follows mutation nomenclature recommendations of Human Genome Variation Society. | Mutation, gene mutation, sequence variations, gene, human NCL disease gene, patient datasheet, mutation datasheet, mutation nomenclature, human genome variation society, data | has parent organization: University College London; London; United Kingdom | Neuronal Ceroid Lipofuscinoses, NCL, Batten disease | Free, Freely available | SCR_018806 | NCL Mutation Database, NCL Mutation and Patient Database | 2026-02-14 02:03:44 | 4 | ||||||||
|
RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | data analysis software, software resource, data processing software, software application | Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data. | Ribo-seq data, analysis, ribosome profiling experiment, triplet periodicity, ribosomal footprint, translated region, three nucleotide periodicity, data, ribosome profiling, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIGMS R01 GM104962; Berlin Institute for Medical Systems Biology |
PMID:26657557 | Free, Freely available | biotools:ribotaper | https://bioconda.github.io/recipes/ribotaper/README.html https://bio.tools/ribotaper |
SCR_018880 | 2026-02-14 02:03:26 | 8 | ||||||
|
reshape Resource Report Resource Website 1+ mentions |
reshape (RRID:SCR_018983) | data processing software, data analysis software, software toolkit, software application, software resource | Software R package for flexibly restructuring and aggregating data. | Data restructuring, data aggregation, flexible data restructuring, data |
is related to: CRAN is related to: reshape2 |
Free, Freely available | SCR_018983 | reshape 0.8 | 2026-02-14 02:03:27 | 4 | |||||||||
|
Annotree Resource Report Resource Website 10+ mentions |
Annotree (RRID:SCR_018980) | data access protocol, data or information resource, software resource, web service | Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes. | Genome annotation, genome visualization, phylogenetic tree, functionally annotated tree, microbial tree of life, taxonomic data, phylogenetic data, functionally annotated data, bacterial genome, archaeal genome, genome distribution, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Ontario Early Researcher award ; NSERC Discovery Grant ; Australian Research Council Laureate Fellowship ; Tier II Canada Research Chair ; Natural Sciences and Engineering Research Council of Canada |
PMID:31081040 | Free, Freely available | biotools:Annotree | https://bio.tools/AnnoTree | SCR_018980 | AnnoTree 1.2 | 2026-02-14 02:03:44 | 22 | |||||
|
ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | data visualization software, data processing software, data analysis software, software application, software resource | Software Python package for analysis of trajectories in clinical datasets. | Trajectories analysis, clinical datasets, analysis, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:clintrajan | https://bio.tools/clintrajan | SCR_019018 | 2026-02-14 02:03:44 | 1 | ||||||||
|
scPancMeta App Resource Report Resource Website 1+ mentions |
scPancMeta App (RRID:SCR_018939) | data or information resource, portal, topical portal | Portal for islet research community. Data for eight scRNA-seq datasets are combined to give consensus overview of islet cell type defining genes. Tools are provided for interacting with and comparing novel genesets generated. | Islet cell, islet genes, data, scRNAseq datasets, islet cell type, gene set generation, gene set comparison, data, islet | is related to: Human Islet Research Network (HIRN) | Restricted | SCR_018939 | 2026-02-14 02:03:27 | 1 | ||||||||||
|
CFTR2 Resource Report Resource Website 100+ mentions |
CFTR2 (RRID:SCR_019078) | portal, data or information resource, disease-related portal, database, topical portal | International initiative led by team of researchers and clinicians and supported by the US Cystic Fibrosis Foundation that seeks to provide complete, advanced and expert reviewed functional and clinical information on CFTR mutations. Provides information for patients, researchers, and general public about specific variants. For each variant or variant combination included in database, website will provide information about whether variant or variant combination is CF-causing, and information about sweat chloride, lung function, pancreatic status, and Pseudomonas infection rate in patients in CFTR2 database with this variant or variant combination. | CF gene, cystic fibrosis gene, functional testing, CFTR2 variant, data, CFTR mutations, clinical information, , FASEB list | is related to: Cystic Fibrosis Mutation Database | cystic fibrosis | Free, Freely available | SCR_019078 | Clinical and Functional TRanslation of CFTR, cftr2, Clinical and Functional TRanslation 2 | 2026-02-14 02:03:48 | 127 | ||||||||
|
D-EE Resource Report Resource Website 1+ mentions |
D-EE (RRID:SCR_019058) | data visualization software, data processing software, data analysis software, software application, software resource | Software tool for distributed dimensionality reduction and visualization. Distributed software for visualizing intrinsic structure of large scale single cell data written in C language. Its distributed storage and distributed computation technique allows efficiently analyze large scale single cell data at cost of constant time speedup. | Distributed dimensionality reduction, dimensionality reduction, distributed storage, distributed computation, large scale data, single cell data, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:d-ee | https://bio.tools/d-ee | SCR_019058 | 2026-02-14 02:03:45 | 1 | ||||||||
|
riboSeqR Resource Report Resource Website 1+ mentions |
riboSeqR (RRID:SCR_016947) | data analysis software, software resource, data processing software, software application | Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments. | analysis, sequencing, data, ribosome, profiling, experiment, plotting, function, frameshift, detect, parsing |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016947 | 2026-02-14 02:03:06 | 4 | ||||||||||
|
Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | data processing software, alignment software, data analysis software, software application, software resource, image analysis software | Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. | sequence, alignment, counting, multi, seed, strategy, mapping, read, reference, genome, analysis, data, SNP, calling, mutation, discovery, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: Subread |
Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | 2026-02-14 02:03:21 | 188 | ||||||
|
scran Resource Report Resource Website 50+ mentions |
scran (RRID:SCR_016944) | SCRAN | data analysis software, software resource, data processing software, software application | Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection. | low, level, analysis, scRNA-seq, data, normalization, cell, cycle, phase, gene, variable, correlation, cluster, subpopulation, marker, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Cancer Research UK ; National Health and Medical Research Council of Australia ; EMBL |
PMID:27909575 | Free, Available for download, Freely available | biotools:scran | https://bio.tools/scran | SCR_016944 | Single-Cell Rna-seq data ANalysis, SCRAN | 2026-02-14 02:03:11 | 92 | ||||
|
OptiQuant Software Resource Report Resource Website 1+ mentions |
OptiQuant Software (RRID:SCR_016769) | data processing software, data acquisition software, image acquisition software, data analysis software, software application, software resource, image analysis software | Software package for image acquisition, analysis, display, and archiving. Used to quantify the autoradiography data from Cyclone apparatus from Perkin Elmer. | image, acquisition, analysis, display, archiving, quantify, autoradiography, data, PerkinElmer | Commercially available, Free download available | https://optiquant.software.informer.com/5.0/ | SCR_016769 | OptiQuant, OptiQuant 3.0, OptiQuant software 5.0, OptiQuant 5.0 | 2026-02-14 02:03:05 | 4 | |||||||||
|
mixOmics Resource Report Resource Website 50+ mentions |
mixOmics (RRID:SCR_016889) | data analysis software, software resource, data processing software, software application | Software R package of multivariate methods for the exploration and integration of biological datasets with a focus on variable selection. Used to analyse data from high throughput sequencing technologies and spectral imaging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multivariate, exploration, integration, biological, dataset, variable, selection, analysis, data, high, throughput, sequencing, technology, spectral, imaging |
is related to: R Project for Statistical Computing has parent organization: University of Melbourne; Victoria; Australia |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016889 | 2026-02-14 02:03:10 | 58 | ||||||||||
|
BISE Resource Report Resource Website 10+ mentions |
BISE (RRID:SCR_016774) | portal, analysis service resource, data or information resource, production service resource, organization portal, service resource, software resource, database | Web platform for bio image analysis. Used to share knowledge between the different communities, to help biologists to find any tool or workflow available for a particular image analysis problem and to find the adequate image processing wording, to help software and algorithm developers to find missing tools (or components), and to help bioimage analyst to identify and edit workflows. | bioimage, analysis, data, information, image, processing, algorithm, workflow, bio.tools |
lists: FibrilTool is listed by: Debian is listed by: bio.tools has parent organization: NEUBIAS |
Free, Freely available, Registration required | biotools:BISE | https://bio.tools/BISE | SCR_016774 | 2026-02-14 02:03:06 | 12 |
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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
