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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
metabnorm Resource Report Resource Website |
metabnorm (RRID:SCR_001266) | software application, software resource, standalone software | Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix. | Metabolomics datasets, corelation, normalization, identifying metabolites, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
Cancer Research UK Cambridge Institute ; Cancer Research UK ; Erik and Edith Fernström foundation |
PMID:24711654 | Free, Available for download, Freely available | OMICS_03548, biotools:metabnorm | https://bio.tools/metabnorm | SCR_001266 | SciCrunch Registry | 2026-11-07 12:03:29 | 0 | ||||||
|
MIGen Resource Report Resource Website 10+ mentions |
MIGen (RRID:SCR_006959) | MIGen | data or information resource, knowledge environment, narrative resource, standard specification | Standard specification for the information required to report a genotyping experiment, covering: study and experiment design, subject information, genotyping procedure, and data analysis methods. The goal is to set a reporting standard for adoption by the research community to facilitate consistent data interpretation and independent validation/reproduction, and to serve as guidance for database design for storing genotyping experiment data. MIGen is being developed as a collaborative project involving international domain experts and is a registered project under MIBBI: Minimum Information for Biological and Biomedical Investigations. | genotyping, genotype, genotyping experiment, data archiving, data management, data sharing, data transfer, data analysis, experiment |
is listed by: OMICtools is related to: Minimum Information for Biological and Biomedical Investigations has parent organization: SourceForge has parent organization: UT Southwestern Medical Center Department of Pathology |
The community can contribute to this resource | OMICS_01786 | SCR_006959 | SciCrunch Registry | Minimum Information about a Genotyping Experiment | 2026-11-07 12:00:15 | 20 | |||||||
|
SAM format Resource Report Resource Website 1000+ mentions |
SAM format (RRID:SCR_012093) | data or information resource, interchange format, narrative resource, standard specification | A generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19505943 | OMICS_05115 | SCR_012093 | SciCrunch Registry | Sequence Alignment/Map format | 2026-11-07 12:00:49 | 1274 | |||||||||
|
HOLLOW Resource Report Resource Website 10+ mentions |
HOLLOW (RRID:SCR_005729) | HOLLOW | data processing software, data visualization software, software application, software resource | HOLLOW facilitates the production of surface images of proteins. HOLLOW is a portable command-line utility written in Python 2.4-2.7; it does not have any other dependencies (although running under the PyPy JIT interpreter, it runs much faster). The input is a PDB file. The output is a PDB file of dummy water atoms that forms a cast of the voids and channels of a protein. HOLLOW generates a surface from a cast of the protein surface. HOLLOW fills the interior spaces of a protein structure with dummy atoms defined on an overlapping grid. The surface generated by these dummy atoms can be shown to reproduce the surface of the protein at the ideal limit. The use of the surface of the dummy atoms allows us to focus on a specific piece of the interior surface. Simply by deleting dummy atoms, the interior surface can be trimmed to produce a custom portion of the interior space. For advanced coloring of the surface, the B-factor of the dummy atoms can be calculated as the average of the B-factor of the protein atoms surrounding the dummy atoms. This allows various colorings of the surface to be conveyed through the B-factor field of the PDB files. The volume filling representation facilitated by HOLLOW is meant to complement other programs that identify voids, pockets and channels, such as SPHGEN and CASTp, which identify binding sites but cannot produce output that can be rendered in standard molecular graphics software. HOLLOW can be used to help render these binding pockets. | surface image, protein, protein image, protein structure, image, channel surface, electrostatic surface, interior pathway surface, ligand-binding surface, molecular structure, python |
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of California at San Francisco; California; USA has parent organization: SourceForge |
Center for Membrane Protein Structure ; Membrane Protein Expression Center ; Howard Hughes Medical Institute |
PMID:19014592 | nlx_149186 | SCR_005729 | SciCrunch Registry | HOLLOW - Volume Filling of Protein Structures, HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures | 2026-11-07 12:00:42 | 37 | ||||||
|
Xournal Resource Report Resource Website |
Xournal (RRID:SCR_003233) | Xournal | software application, software resource | Free software application for notetaking, sketching, keeping a journal using a stylus that runs on Linux (recent distributions) and other GTK+/Gnome platforms. It is similar to Microsoft Windows Journal or to other alternatives such as Jarnal, Gournal, and NoteLab. Note: is open source and allows some annotation, but its PDF reading ability is very limited. It also uses its own format to store annotations. | annotation, markup |
is listed by: FORCE11 has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_157272 | SCR_003233 | SciCrunch Registry | 2026-11-07 12:03:29 | 0 | ||||||||
|
TARQUIN Resource Report Resource Website 50+ mentions |
TARQUIN (RRID:SCR_002598) | TARQUIN | software application, software resource | An analysis tool for automatically determining the quantities of molecules present in NMR spectroscopic data. The intended purpose of TARQUIN is to aid the characterisation of pathologies, in particular brain tumours, both non-invasively with in-vivo 1H MRS and ex-vivo with 1H HR-MAS. TARQUIN has the following features: * Free to use and modify under the GPL licence. * Based on a flexible time-domain fitting routine designed to give accurate rapid and automated quantitation for routine analysis. * Cross platform, works on Windows, Linux and OSX. * Comes packaged with a quantum mechanically based metabolite simulator to allow basis set construction optimised for the investigation of particular pathologies sequence parameters. * Includes both GUI and command line interface for one-off and batch analyses. | magnetic resonance, mrs, mas, molecule, nmr spectroscopy |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
PMID:20878762 | Free, Available for download, Freely available | nlx_156002 | http://www.nitrc.org/projects/tarquin | SCR_002598 | SciCrunch Registry | TARQUIN MRS analysis package | 2026-11-07 12:03:29 | 64 | |||||
|
HTQC Resource Report Resource Website 10+ mentions |
HTQC (RRID:SCR_006448) | HTQC | software resource, software toolkit | A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc.. | c++, illumina, command-line |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:23363224 DOI:10.1186/1471-2105-14-33 |
GNU General Public License, v3 | OMICS_01052 | https://sources.debian.org/src/htqc/ | SCR_006448 | SciCrunch Registry | HTQC - Quality control and filtration for illumina sequencing data | 2026-11-07 12:03:36 | 43 | |||||
|
MarsBaR region of interest toolbox for SPM Resource Report Resource Website 1000+ mentions |
MarsBaR region of interest toolbox for SPM (RRID:SCR_009605) | MarsBaR | data processing software, software application, software resource, software toolkit | A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery. | analyze, linear, matlab, magnetic resonance, nifti, os independent, regression, statistical operation, region of interest, spm, analysis |
is used by: BetA-Series COrrelation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: SourceForge |
GNU General Public License | nlx_155806 | http://www.nitrc.org/projects/marsbar | SCR_009605 | SciCrunch Registry | MARSeille Boite A Region dInteret, MARSeille Boite a Region dInteret | 2026-11-07 12:01:33 | 1320 | ||||||
|
Avalon Cheminformatics Toolkit Resource Report Resource Website |
Avalon Cheminformatics Toolkit (RRID:SCR_014273) | software resource, software toolkit | Software toolkit containing tools to render and canonicalize SMILES and manipulate MOL file and related formats, as well as structure fingerprinting. | software toolkit, chemistry, canonicalize smiles, render smiles, manipulate mol file, structure fingerprinting | is listed by: SourceForge | Free, Available for download | SCR_014273 | SciCrunch Registry | 2026-11-07 12:03:50 | 0 | ||||||||||
|
BVA import/export EEGLAB plugin Resource Report Resource Website 1+ mentions |
BVA import/export EEGLAB plugin (RRID:SCR_016333) | bva-io | software application, software resource, software toolkit | Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software. | interfacing, brain, vision, analyser, data, file, load, save, Matlab, routine, compatible, EEGLAB |
is related to: SourceForge is related to: EEGLAB is related to: MATLAB |
Free, Available for download, Freely available | SCR_016333 | SciCrunch Registry | Brain Vision Analyser | 2026-11-07 12:03:56 | 4 | ||||||||
|
cnvHiTSeq Resource Report Resource Website 1+ mentions |
cnvHiTSeq (RRID:SCR_013160) | cnvHiTSeq | commercial organization, software resource | A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23259578 | Commercial license | OMICS_00342 | SCR_013160 | SciCrunch Registry | cnvHiTSeq - A set of tools for detecting CNVs using sequencing data | 2026-11-07 12:05:20 | 4 | ||||||
|
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | SciCrunch Registry | 2026-11-07 12:04:21 | 35 | ||||||
|
Picard Resource Report Resource Website 10000+ mentions Rating or validation data |
Picard (RRID:SCR_006525) | software resource, software toolkit, source code | Java toolset for working with next generation sequencing data in the BAM format. | next generation sequencing, java, bam |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge has parent organization: Broad Institute is required by: SL-quant |
Available for download, Free | OMICS_01066 | http://sourceforge.net/projects/picard/, https://github.com/broadinstitute/picard, https://sources.debian.org/src/picard-tools/ | SCR_006525 | SciCrunch Registry | 2026-11-07 12:04:42 | 15653 | ||||||||
|
neurospy Resource Report Resource Website |
neurospy (RRID:SCR_007016) | neurospy | software resource, source code | neurospy is a free software for functional imaging of fast neuronal activity. neurospy is a modular cross-platform application framework written in Java for the NetBeans Platform. At this time it runs on Windows XP-based LeCroy oscilloscopes and drives acousto-optic scanners via USB using the Analog Devices 9959 Direct Digital Synthesis chip. This combination makes one of the most powerful systems for scanning microscopy available today at any price. neurospy is very easy to port to other kinds of acquisition and scanning hardware. | imaging, neuron, microscopy, functional imaging, java, neuronal activity |
has parent organization: SourceForge has parent organization: Howard Hughes Medical Institute has parent organization: Salk Institute for Biological Studies has parent organization: University of California at San Diego; California; USA |
Howard Hughes Medical Institute ; NIH |
PMID:17684546 | Open unspecified license | nlx_149367 | SCR_007016 | SciCrunch Registry | 2026-11-07 12:04:17 | 0 | ||||||
|
CUDASW++ Resource Report Resource Website 1+ mentions |
CUDASW++ (RRID:SCR_008862) | CUDASW++ | software resource, source code | CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher | smith-waterman, bioinformatics, protein, protein database, sequence, simt, simd, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Nanyang Technological University; Singapore; Singapore |
PMID:19416548 PMID:20370891 |
Open-source | nlx_149212, biotools:cudasw | https://bio.tools/cudasw | SCR_008862 | SciCrunch Registry | CUDASW++ (Smith Waterman) | 2026-11-07 12:04:31 | 5 |
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.
