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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_016492) | software application, software resource, data analysis software, data processing software | 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 | 2026-07-28 09:44:15 | 4 | |||||||
|
PiGx Resource Report Resource Website 1+ mentions |
PiGx (RRID:SCR_016476) | PiGx | software application, data analysis software, sequence analysis software, software resource, data processing software, software toolkit | 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 | 2026-07-28 09:44:18 | 6 | |||||||
|
Transcriptome Analysis Console Resource Report Resource Website 10+ mentions |
Transcriptome Analysis Console (RRID:SCR_016519) | TAC | software application, data analysis software, sequence analysis software, software resource, data processing 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 | 2026-07-28 09:44:20 | 19 | |||||||||
|
Viewbox4, Cephalometric software Resource Report Resource Website 1+ mentions |
Viewbox4, Cephalometric software (RRID:SCR_016481) | software application, data analysis software, software resource, data processing software, image 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 | 2026-07-28 09:44:19 | 5 | |||||||||||
|
SwarmSight Resource Report Resource Website |
SwarmSight (RRID:SCR_016451) | software application, data analysis software, software resource, data processing software, image 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 | 2026-07-28 09:44:18 | 0 | ||||||||||
|
Image Studio Lite Resource Report Resource Website 100+ mentions |
Image Studio Lite (RRID:SCR_013715) | software application, software resource, data analysis software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 28,2023. Software application which can analyze basic Western blot data and export them for use in spreadsheet programs. Users can create standardized or custom lab reports and can share them with colleagues. Image Studio Lite has been discontinued and replaced with Empiria Studio Software. | Li-COR, Odyssey, infrared, immunoblot, western blot, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014211 | SCR_013715 | Image Studio Lite version 3.1, LICOR Image Studio Lite Software, LI-COR Image Studio Lite Software, Image Studio Lite Software | 2026-07-28 09:43:18 | 256 | |||||||||
|
HED Tags Resource Report Resource Website 1+ mentions |
HED Tags (RRID:SCR_014074) | HED | data or information resource, narrative resource, standard specification | Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging. | Data, structure, standard, EEG, brain, imaging, comma, separated, path, string, analysis, MEG, fNIRS, multimodal, ECG, EMG, GSR, behavioral, BRAIN Initiative |
is used by: NIMH Data Archive is used by: HeadIT is used by: OpenNeuro is recommended by: BRAIN Initiative has parent organization: University of California at San Diego; California; USA |
Swartz Foundation ; Army Research Laboratory Cooperative Agreement ; NIMH R01MH084819; NINDS R01 NS047293 |
PMID:27799907 | Free, Freely available | SCR_017630 | SCR_014074 | Hierarchical Event Descriptor Tags, Hierarchical Event Descriptor, HED, HED tags | 2026-07-28 09:43:41 | 7 | |||||
|
Skyline Resource Report Resource Website 1000+ mentions |
Skyline (RRID:SCR_014080) | software application, software resource, data analysis software, data processing software | Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences. | Proteomics, SRM, MRM, DDA, DIA, shotgun, mass, spectrometry, data, analysis, quantitative |
uses: MSstats is related to: ProteoWizard has parent organization: University of Washington; Seattle; USA works with: PanoramaWeb |
NCI U24 CA126479; NIDDK R01 DK069386; NCRR P41 RR011823; NIA P30 AG013280; NHLBI R01 HL082747 |
PMID:20147306 | Free, Available for download, Freely available | SCR_014080 | 2026-07-28 09:43:23 | 2805 | ||||||||
|
Origin Resource Report Resource Website 10000+ mentions |
Origin (RRID:SCR_014212) | software application, data analysis software, software resource, data processing software, data visualization software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing. | data, analysis, software, authoring, tool, scripting, graphing, statistical, publication |
is listed by: SoftCite is related to: OriginPro |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015636 | https://www.originlab.com/index.aspx?go=PRODUCTS&PID=1834 | SCR_014212 | OriginPro | 2026-07-28 09:43:25 | 13956 | |||||||
|
Maple Resource Report Resource Website 100+ mentions |
Maple (RRID:SCR_014449) | software application, software resource, data analysis software, data processing software | Mathematical software that can compute both numeric and symbolic solutions. It can be used to analyze, explore, visualize, and solve mathematical problems. | math, analysis, mathmatics, computation, meta-analysis, numeric, symbolic | SCR_014449 | Maple Software, Maplesoft, Maple Soft, MapleSoft | 2026-07-28 09:43:26 | 148 | |||||||||||
|
Wolfram Mathematica Resource Report Resource Website 100+ mentions |
Wolfram Mathematica (RRID:SCR_014448) | software application, data processing software, software resource, data visualization software, data analytics software, data storage software | A technical computing software and computing environment that provides users with algorithms and mathematical functions for various projects and purposes. The resource incorporates other Wolfram products such as Wolfram Algorithmbase, Wolfram Language, and Wolfram Knowledgebase. | analysis, computing, machine learning, wolfram notebook, meta-algorithm, cloud | Commercial product | SCR_014448 | 2026-07-28 09:43:52 | 488 | |||||||||||
|
VolView Resource Report Resource Website 50+ mentions |
VolView (RRID:SCR_014569) | software application, data or information resource, software resource, data processing software, image processing software, image, 3d spatial image, image analysis software | A software for volume visualization that can be used by researchers to explore and analyze medical and scientific data. This software uses a variety of tools to load and visualize the data on either a 2D or 3D display. Theses tools include volume rendering, maximum intensity projections and oblique reformatting. Visualizations can be saved mid-session and be reopened at a later time. | volume visualization, volume, analysis, 2d, 3d, volume, rendering, intensity, oblique reformatting, visualization, volume rendering, rendering software |
uses: VTK has parent organization: Kitware |
Open Source | SCR_014569 | 2026-07-28 09:43:53 | 61 | ||||||||||
|
FactoMineR Resource Report Resource Website 1000+ mentions |
FactoMineR (RRID:SCR_014602) | software application, software resource, data analysis software, data processing software | Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables. | multivariate, analysis, data, structure, organized, group, variable, individual, hierarchy |
is used by: ClustVis is listed by: CRAN |
https://cran.r-project.org/web/packages/FactoMineR/index.html, https://github.com/husson/FactoMineR | SCR_014602 | factominer | 2026-07-28 09:43:32 | 2349 | |||||||||
|
FastQC Resource Report Resource Website 10000+ mentions Rating or validation data |
FastQC (RRID:SCR_014583) | software application, data analysis software, software resource, data management software, data processing software | Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis. | quality control, sequence data, sequencing, analysis, data quality, pipeline, raw sequence data, modular set, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Open source, Available for download | biotools:fastqc, SCR_005539, OMICS_01043 | https://omictools.com/fastqc-tool, https://bio.tools/fastqc, https://sources.debian.org/src/fastqc/ | SCR_014583 | FastQC v0.11.5 | 2026-07-28 09:43:54 | 18745 | |||||||
|
OmniPlex Software Resource Report Resource Website 10+ mentions |
OmniPlex Software (RRID:SCR_014803) | software application, data processing software, software resource, data visualization software, data acquisition software | Neural data acquisition software for signal visualization in neuron recordings along with spike wave-form classification methods. It is made up of the PlexControl software program and the OmniPlex Server. | software, neural, neuron data, analysis, pca, data acquisition, signal visualization | Commercially available | SCR_014803 | 2026-07-28 09:43:33 | 25 | |||||||||||
|
Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility (RRID:SCR_014868) | SBP MDI Bioinformatics and Data Management Facility, SBP Medical Discovery Institute Bioinformatics and Data Management Facility, SBP MDI Bioinformatics and Data Management Facility | service resource, group, training core facility, software resource, computational hosting, access service resource, core facility | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 11132025. Facility that provides database development and management and bioinformatic network building services by utilizing on-site hardware and software. Three members of the facility are available to assist researchers with advanced bioinformatics and biostatistics analysis to help put data into biological context across various disease areas to create testable hypotheses and understand biology of the process. The bulk of support includes connecting functional genomic data with pathways and networks, connecting gene/protein expression and disease state and consultations on statistical aspects of the research with the team statistician. | data, management, database, bioinformatic, network, connectivity, statistics, analysis, biostatistics, pipeline, software | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_014868 | SBP, , Data Management Facility, MDI, Medical Discovery Institute, Sanford Burnham Prebys, Bioinformatics | 2026-07-28 09:43:34 | 0 | |||||||||
|
HeteroAnalysis Resource Report Resource Website 50+ mentions |
HeteroAnalysis (RRID:SCR_014991) | software application, data analysis software, algorithm resource, software resource, data processing software | Software for analyzing sedimentation equilibrium (SE) data from analytical ultracentrifugation experiments. It uses a model-dependent simulation of data for matching data in order to determine when equilibrium has been achieved. | sedimentation equilibrium, ultracentrifugation, analysis, model dependent | has parent organization: University of Connecticut; Connecticut; USA | Available for download | http://core.uconn.edu/files/auf/ha-help/HA-Help.htm | SCR_014991 | HeteroAnalysis Version 1.1.0.58 | 2026-07-28 09:43:36 | 62 | ||||||||
|
NetPyNE Resource Report Resource Website 10+ mentions |
NetPyNE (RRID:SCR_014758) | software application, data analysis software, software resource, data processing software, network analysis software | Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks. | Simulation, analysis, neuronal, network, NEURON, simulator, BRAIN Initiative |
uses: Python Programming Language is recommended by: BRAIN Initiative works with: NEURON |
NIBIB EB022903 | DOI:10.7554/eLife.44494.001 | Free, Available for download, Freely available | http://www.neurosimlab.org/netpyne/overview.html | SCR_014758 | Network development Python package for NEURON | 2026-07-28 09:43:35 | 26 | ||||||
|
Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | software application, data analysis software, sequence analysis software, software resource, data processing software, alignment software, image analysis software | Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method. | sequence, analysis, long, reference, sequence, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: HLA-HD is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Bowtie |
NHGRI R01 HG006102; NIGMS R01 GM083873 |
PMID:22388286 | Free, Available for download, Freely available | biotools:bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml, https://github.com/BenLangmead/bowtie2, https://bio.tools/bowtie2 | SCR_016368 | , bowtie 2, bowtie2 v 2.2.3 | 2026-07-28 09:43:31 | 1745 | |||||
|
RTCA Software Resource Report Resource Website 10+ mentions |
RTCA Software (RRID:SCR_014821) | software application, data analysis software, software resource, data processing software, data acquisition software | Data acquisition and analysis software used for xCELLigence Real Time Cell Analysis SP, DP and MP instruments. The software is used to program and execute experiments and analyze data. | system management software, cell, analysis, real time, data acquisition, data analysis | Commercially available | SCR_014821 | Real Time Cell Analysis (RTCA) Software, Real Time Cell Analysis Software, RTCA 2.0 Software | 2026-07-28 09:43:36 | 23 |
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.
