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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Splicing Express Resource Report Resource Website 1+ mentions |
Splicing Express (RRID:SCR_016498) | software application, data visualization software, data processing software, software resource, data analysis software | Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems. | alternative, splicing, analysis, next, generation, sequencing, data, transcriptome, identify, annotate, visualize, Perl, UNIX, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:26618088 | Free, Available for download, Freely available | biotools:splicing_express | https://bio.tools/splicing_express | SCR_016498 | 2026-02-15 09:21:42 | 3 | |||||||
|
SARTools Resource Report Resource Website 100+ mentions |
SARTools (RRID:SCR_016533) | software application, data processing software, software resource, software toolkit, data analysis software | Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data. | R package, DESeq2, EdgeR, comprehensive, analysis, RNAseq, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: DESeq2 is related to: edgeR has parent organization: Pasteur Institute |
the France Génomique National Infrastructure | PMID:27280887 | Free, Available for download, Freely available | biotools:sartools | https://bio.tools/sartools | SCR_016533 | 2026-02-15 09:21:07 | 136 | ||||||
|
TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_016492) | software application, data processing software, data analysis software, software resource | Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. | statistical, analysis, TnSeq, data, identify, gene, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Texas A and M University; Texas; USA |
PMID:26447887 | Free, Available for download, Freely available | biotools:transit | https://github.com/mad-lab/transit https://bio.tools/transit |
SCR_016492 | 2026-02-15 09:21:07 | 4 | |||||||
|
PiGx Resource Report Resource Website 1+ mentions |
PiGx (RRID:SCR_016476) | PiGx | software application, sequence analysis software, data processing software, software resource, software toolkit, data analysis software | Software application as a collection of genomic pipelines used for raw fastq read data of bisulfite experiments, RNAseq samples, single cell dropseq analysis, reads from ChIPseq experiments, analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data. | collection, genomic, pipeline, bisulfite, sequencing, rnaseq, chipseq, single, cell, reproducibility, sample, analysis, mutation, data | German Federal Ministry of Education and Research (BMBF) 031 A538C RBC (de.NBI); European Union Horizon 2020 No 654248 |
Free, Available for download, Freely available | https://github.com/BIMSBbioinfo/pigx | SCR_016476 | Pipelines in Genomics | 2026-02-15 09:21:41 | 6 | |||||||
|
biobakery Resource Report Resource Website 10+ mentions |
biobakery (RRID:SCR_016596) | software application, data processing software, software resource, software toolkit, data analysis software | Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Huttenhower lab, metaomics, data, analysis, process, raw, shotgun, metagenome, metatranscriptome, sequencing, microbial, profiling, bio.tools |
is used by: Nephele is listed by: Debian is listed by: bio.tools is related to: Human Microbiome Project has parent organization: Harvard University; Cambridge; United States |
NIDDK U54 DE023798; Sloan Foundation 4406J0B; NHGRI R01 HG005220; NSF DBI1053486; NHGRI R01 HG005969; ARO W911NF1110473 |
PMID:29194469 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:biobakery | http://huttenhower.sph.harvard.edu/biobakery https://bio.tools/biobakery |
SCR_016596 | bioBakery, biobakery | 2026-02-15 09:21:53 | 13 | |||||
|
rsfMRI_fconn calculation Resource Report Resource Website 1+ mentions |
rsfMRI_fconn calculation (RRID:SCR_016591) | rsfMRI_fconn calculation | software application, data processing software, data analysis software, software resource | Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity. | data, resting, state, brain, processing, functional, magnetic, resonance, imaging, measurement, calculate, region, connectivity, analysis, sequence |
uses: SPM is related to: MATLAB |
SCR_016591 | resting state functional MRI and functional connectivity calculation, resting state functional MRI pre processing and Functional Connectivity calculation | 2026-02-15 09:21:53 | 1 | |||||||||
|
Transcriptome Analysis Console Resource Report Resource Website 10+ mentions |
Transcriptome Analysis Console (RRID:SCR_016519) | TAC | software application, sequence analysis software, data processing software, software resource, data analysis software | Software tool for microarray analysis designed for biologists . Used for identification of differential expression by providing interactive visualizations. | transcriptome, analysis, console, data, array, gene, visualization, identify | Commercially available | SCR_016519 | TAC:Transcriptome Analysis Console | 2026-02-15 09:21:42 | 19 | |||||||||
|
Viewbox4, Cephalometric software Resource Report Resource Website 1+ mentions |
Viewbox4, Cephalometric software (RRID:SCR_016481) | software application, data processing software, software resource, image analysis software, data analysis software | Software for cephalometric analysis. Customizable. Allows rendering, viewing and measuring of 3D data from CT scanners. Used in orthodontic departments for analysis of the dental and skeletal relationships of a human skull. | dHAL Software - The Company, cephalometric, analysis, rendering, viewing, measuring, data, CT scan, orthodontic, dental, skeletal, relationship, human, skull | Commercially available, Tutorial available | SCR_016481 | 2026-02-15 09:21:41 | 5 | |||||||||||
|
PhenoMeNal Resource Report Resource Website 1+ mentions |
PhenoMeNal (RRID:SCR_016605) | phnmnl, PhenoMeNal | organization portal, portal, software resource, data access protocol, web service, consortium, data or information resource | Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics. | metabolomic, phenomic, data, processing, analysis, information, mining. medical, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory has parent organization: European Bioinformatics Institute |
European Commission EC654241 | Free, Registration required, Tutorial available | biotools:PhenoMeNal | https://github.com/phnmnl https://bio.tools/PhenoMeNal |
SCR_016605 | Phenome and Metabolome aNalysis | 2026-02-15 09:21:53 | 2 | |||||
|
SPICE Resource Report Resource Website 50+ mentions |
SPICE (RRID:SCR_016603) | SPICE | software application, data visualization software, data processing software, software resource, data analysis software | Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically. | data, mining, visualization, analysis, polychromatic, flow, cytometry, dataset, normalized, graphically, bio.tools |
is listed by: NIAID is listed by: Debian is listed by: bio.tools |
NIAID ; NIH |
PMID:21265010 | Free, Available for download, Freely available | biotools:spice | https://bio.tools/spice | SCR_016603 | Simplified Presentation of Incredibly Complex Evaluations | 2026-02-15 09:21:45 | 66 | ||||
|
SwarmSight Resource Report Resource Website |
SwarmSight (RRID:SCR_016451) | software application, data processing software, software resource, image analysis software, data analysis software | Software for video analysis with modules to track insect antenna and proboscis movements. Its purpose is to assess the aggregate movement or activity levels of groups or swarms of animals. | c language, bug, insect, antennae, proboscis, activity, research, subject, swarm, behavior, tracking, video, analysis | Free, Available for download, Acknowledgement requested | SCR_016451 | SwarmSight Software, Swarm Sight | 2026-02-15 09:21:40 | 0 | ||||||||||
|
MAJIQ Resource Report Resource Website 10+ mentions |
MAJIQ (RRID:SCR_016706) | MAJIQ, | software application, data processing software, software resource, software toolkit, data analysis software | Software package to detect and quantify local splicing variations (LSV) from RNA-Seq data. Used to automatically detect and downweight outliers in RNA-Seq datasets with replicates for differential splicing (SD) analysis. | detect, quantify, local, splicing, variation, RNA-Seq, data, replicate, differential, analysis | has parent organization: University of Pennsylvania; Philadelphia; USA | NIA R01 AG046544; Penn Institute for Biomedical Informatics Pilot |
PMID:29236961 | Free, Available for download, Freely available, Tutorial available | SCR_016706 | MAJIQ, MAJIQ/Viola, Modeling Alternative Junction Inclusion Quantification | 2026-02-15 09:21:47 | 30 | ||||||
|
Motion Sensing Superpixels (MOSES) Resource Report Resource Website 1+ mentions |
Motion Sensing Superpixels (MOSES) (RRID:SCR_016839) | MOSES | software application, data processing software, data analysis software, software resource | Computational Python library for the motion analysis of biological single-cell and collective motion for high content screens. Framework to quantify and discover cellular motion phenotypes. | motion, analysis, biological, single, cell, collective, motion, high, content, screen, quantify, discover, phenotype | DOI:10.1101/248104 | Free, Freely available for academic non commercial research | SCR_016839 | Motion Sensing Superpixels (MOSES), MOSES, Motion Sensing Superpixels | 2026-02-15 09:21:55 | 1 | ||||||||
|
MetaboAnalystR Resource Report Resource Website 100+ mentions |
MetaboAnalystR (RRID:SCR_016723) | software application, data visualization software, data processing software, software resource, data analysis software | Software R package for comprehensive analysis of metabolomics data. Contains the R functions and libraries underlying MetaboAnalyst web server, including functions for metabolomic data analysis, visualization, and functional interpretation. | analysis, metabolomic, data, analysis, vixualization, functional, interpretation | works with: MetaboAnalyst | Natural Sciences and Engineering Research Council of Canada ; Canada Research Chairs ; McGill Graduate Dean Award |
PMID:29955821 | Free, Available for download, Freely available | SCR_016723 | 2026-02-15 09:21:47 | 410 | ||||||||
|
OptiQuant Software Resource Report Resource Website 1+ mentions |
OptiQuant Software (RRID:SCR_016769) | software application, data processing software, software resource, data acquisition software, image analysis software, image acquisition software, data 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 | 2026-02-15 09:21:55 | 4 | |||||||||
|
BISE Resource Report Resource Website 10+ mentions |
BISE (RRID:SCR_016774) | organization portal, portal, database, software resource, service resource, production service resource, data or information resource, analysis service resource | 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 | 2026-02-15 09:21:48 | 12 | ||||||||
|
Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS Resource Report Resource Website 500+ mentions |
Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS (RRID:SCR_016657) | software application, data processing software, software resource, data analytics software, data acquisition software, software toolkit, data analysis software | Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise. | compound, centric, data, mining, navigation, chromatic, separation, coeluting, peak, signal, noise, mass, spectrometry, analysis, qualitative |
is listed by: OMICtools is related to: Agilent Masshunter Quantitative Analysis software has parent organization: Agilent Technologies |
SCR_016657 | 2026-02-15 09:21:54 | 733 | |||||||||||
|
VisR Resource Report Resource Website 1+ mentions |
VisR (RRID:SCR_016658) | VisR | software application, data visualization software, data processing software, software resource, software toolkit, data analysis software | Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses. | visual, framework, analysis, sequencing, data, dataset, integrative, interactive, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor |
Michael Smith Foundation for Health Research ; Canadian Institutes of Health Research (CIHR) and Genome BC ; NSERC PGS-D |
PMID:26328469 | Free, Available for download, Freely available | biotools:VisR | https://bio.tools/VisR | SCR_016658 | VisRseq, VisR | 2026-02-15 09:21:09 | 5 | ||||
|
IndelGenotyper Resource Report Resource Website 50+ mentions |
IndelGenotyper (RRID:SCR_016663) | GATK | software application, sequence analysis software, data processing software, software resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer. | next, generation, analysis, genomic, data, cancer, genome |
is listed by: Debian has parent organization: Broad Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/broadinstitute/gatk/ https://sources.debian.org/src/gatk/ |
SCR_016663 | GATK Indel Genotyper, Genome Analysis Toolkit (GATK) Indel Genotyper, Indel Genotyper, GATK IndelGenotyper | 2026-02-15 09:21:09 | 63 | |||||||
|
Neurolucida 360 Resource Report Resource Website 10+ mentions |
Neurolucida 360 (RRID:SCR_016788) | software application, data processing software, data analysis software, software resource | Software for automatic neuron 3D reconstruction and analysis. Used by neuroscientists to reconstruct intricate neuronal structures that range in scale from complex, multicellular networks of neurons to sub-cellular dendritic spines and putative synapses. | mbf Bioscience, automatic, image, 3D, reconstruction, analysis, neuron, synapse, data | is used by: SPARC Portal | Commercially available, Free trial available | SCR_016788 | 2026-02-15 09:21:49 | 45 |
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.
