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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Easyfig Resource Report Resource Website 1000+ mentions |
Easyfig (RRID:SCR_013169) | Easyfig | software resource | A Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI). |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00907 | SCR_013169 | 2026-02-14 02:02:27 | 1101 | ||||||||||
|
ChimeraSlayer Resource Report Resource Website 100+ mentions |
ChimeraSlayer (RRID:SCR_013283) | ChimeraSlayer | software resource | A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01113, biotools:chimeraslayer | https://bio.tools/chimeraslayer | SCR_013283 | 2026-02-14 02:02:47 | 319 | ||||||||
|
Telescoper Resource Report Resource Website |
Telescoper (RRID:SCR_013206) | Telescoper | software resource | An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22962446 | biotools:telescoper, OMICS_00036 | https://bio.tools/telescoper | SCR_013206 | Telescoper - De novo assembly algorithm | 2026-02-14 02:02:28 | 0 | ||||||
|
palfinder Resource Report Resource Website 1+ mentions |
palfinder (RRID:SCR_013174) | palfinder | software resource | A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads. | pacific biosciences |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00111 | SCR_013174 | 2026-02-14 02:02:46 | 6 | |||||||||
|
sam comp Resource Report Resource Website |
sam comp (RRID:SCR_013179) | sam_comp | software resource | A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533605 | OMICS_00968 | SCR_013179 | 2026-02-14 02:02:46 | 0 | ||||||||
|
HeurAA Resource Report Resource Website |
HeurAA (RRID:SCR_013212) | HeurAA | software resource | Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23349847 | OMICS_00097, biotools:heuraa | https://bio.tools/heuraa | SCR_013212 | heurAA - NGS multiplexed amplicon aligner | 2026-02-14 02:02:28 | 0 | ||||||
|
bisReadMapper Resource Report Resource Website |
bisReadMapper (RRID:SCR_013171) | bisReadMapper | software resource | Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00576 | SCR_013171 | bisReadMapper - Software for dealing with DNA methylation sequencing data | 2026-02-14 02:02:50 | 0 | ||||||||
|
CLIIQ Resource Report Resource Website 1+ mentions |
CLIIQ (RRID:SCR_009972) | CLIIQ | software resource | An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01272 | SCR_009972 | 2026-02-14 02:01:54 | 1 | ||||||||||
|
CHEBI Resource Report Resource Website 100+ mentions |
CHEBI (RRID:SCR_002088) | ChEBI | data or information resource, database | Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. | complex, conformer, ion, ion pair, isotope, molecular entity, molecule, radical, radical ion, small molecule, obo, gold standard, biochemistry, metabolomics, bio.tools |
uses: IUPAC uses: Nomenclature Committee of IUBMB is used by: Open PHACTS is used by: Ultimate Rough Aggregation of Metabolic Map is used by: RHEA is used by: GEROprotectors is used by: SwissLipids is listed by: OBO is listed by: BioPortal is listed by: NIF Data Federation is listed by: SourceForge is listed by: bio.tools is listed by: Debian is related to: Pathway Commons is related to: Integrated Manually Extracted Annotation has parent organization: European Bioinformatics Institute is parent organization of: Physico-Chemical Process is parent organization of: Physico-Chemical Methods and Properties works with: MiMeDB |
BBSRC BB/G022747/1 | PMID:19854951 PMID:19496059 PMID:17932057 |
Freely available | nif-0000-02655, biotools:chebi | http://bioportal.bioontology.org/ontologies/1007 http://www.obofoundry.org/cgi-bin/detail.cgi?id=chebi ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo http://chebi.wiki.sourceforge.net/ https://bio.tools/chebi |
http://www.ebi.ac.uk/chebi/ | SCR_002088 | CHEBI, Chemical Entities of Biological Interest | 2026-02-14 02:06:07 | 126 | |||
|
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 | 2026-02-14 02:07:19 | 35 | ||||||
|
Blox Resource Report Resource Website 1+ mentions |
Blox (RRID:SCR_006667) | Blox | software application, data visualization software, data processing software, software resource, image analysis software | A quantitative medical imaging and visualization program for use on brain MR, DTI, and MRS data. Programming Language: Java, JavaScript, Scheme | magnetic resonance imaging, diffusion tensor imaging, magnetic resonance spectroscopy, 3d visualization, brain, 3d rendering, neuroimaging, registration, segmentation, visualization, volume |
is listed by: Biositemaps has parent organization: SourceForge has parent organization: Kennedy Krieger Institute has parent organization: Johns Hopkins University; Maryland; USA |
GNU General Public License | nif-0000-00270 | http://pni.med.jhu.edu/blox/ | SCR_006667 | 2026-02-15 09:19:32 | 5 | |||||||
|
bioNerDS Resource Report Resource Website 1+ mentions |
bioNerDS (RRID:SCR_006784) | bioNerDS | software application, source code, data set, software resource, text-mining software, data or information resource | A named entity recognizer for the recovery of bioinformatics databases and software from primary literature. The entity recognizer achieved an F-measure of between 63% and 91% on different datasets (63%78% at the document level). Results from full-text literature analysis for both Genome Biology and BMC Bioinformatics journals are available as well as a full list of references and links for the various major resources mentioned. Data generated data can be used for exploration of bioinformatics database and software usage. This tool makes heavy use of GATE (version 6.1). It can be run in sandbox mode, which means a installation of GATE is not a prerequisite, but you will instead need to point the config to a unzipped gate_plugins directory instead (located in the bin/BMC_Files directory). | literature mining, bioinformatics, database, software, resource |
has parent organization: SourceForge has parent organization: University of Manchester; Manchester; United Kingdom |
BBSRC | PMID:23768135 | Open-source license, Acknowledgement requested, Source code, Simplified BSD License, All included libraries retain their own respective licenses. Some source code from other projects has been used/adapted for inclusion in this project (e.g., LINNAEUS, JCommander, JOrtho, GATE and Snowball). Attribution for these remains with the original respective authors, And is distributed in accordance with their own licenses. | nlx_152793 | SCR_006784 | Bioinformatics Named Entity Recognizer for Databases and Software, Bioinformatics Named Entity Recogniser for Databases and Software | 2026-02-15 09:19:19 | 3 | |||||
|
Jmol Resource Report Resource Website 100+ mentions |
Jmol (RRID:SCR_003796) | Jmol | software application, d visualization software, standalone software, software resource | An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems and features an applet, application, and systems integration component. | chemical, crystal, material, biomolecule, java |
is used by: Glyco3D is listed by: SoftCite has parent organization: SourceForge |
PMID:28472503 PMID:28316648 |
GNU Lesser General Public License, Acknowledgement requested | nlx_158093 | SCR_003796 | Jmol: an open-source Java viewer for chemical structures in 3D | 2026-02-15 09:18:37 | 233 | ||||||
|
DeconSeq Resource Report Resource Website 100+ mentions |
DeconSeq (RRID:SCR_007006) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software tool to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. The user can upload FASTA or FASTQ files and select the databases used for contamination screening, including seven human genomes, bacterial genomes, and viral genomes. The user can set the thresholds interactivly and see the results directly using the functionality of the graphical interface. The results can be downloaded in joined or separated files in different formats. The coverage-identity plots provide additional information that can guide the selections of the thresholds using color coded points and connecting lines. | microbiome, sequence analysis, genomic, metagenomic, datasets, contamination, decontamination, FASEB list |
is listed by: OMICtools is listed by: Human Microbiome Project has parent organization: SourceForge |
Available for download | OMICS_01418 | SCR_007006 | DECONtamination of SEQuence data, decontamination of sequence data | 2026-02-15 09:19:26 | 209 | ||||||||
|
Monte Carlo eXtreme Resource Report Resource Website 1+ mentions |
Monte Carlo eXtreme (RRID:SCR_007001) | MCX | software application, simulation software, software resource | A Monte Carlo simulation software for photon migration in 3D turbid media. It uses Graphics Processing Units (GPU) based massively parallel computing techniques and is extremely fast compared to the traditional single-threaded CPU-based simulations. Using an nVidia 8800GT graphics card (14MP/114Cores), the acceleration is about 300x~400x compared to a single core of Xeon 5120 CPU; this ratio can be as high as 700x with a GTX 280 GPU and 1400x with a GTX 470. | c, console (text based), macos, microsoft, modeling, monte carlo, optical imaging, other programming language, posix/unix-like, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
GNU General Public License | nlx_155817 | http://www.nitrc.org/projects/mcextreme | SCR_007001 | Monte Carlo eXtreme (MCX) | 2026-02-15 09:19:25 | 2 | ||||||
|
Multiscale Object Orientation Simulation Environment Resource Report Resource Website 100+ mentions |
Multiscale Object Orientation Simulation Environment (RRID:SCR_008031) | software application, simulation software, software resource | MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology. MOOSE spans the range from single molecules to subcellular networks, from single cells to neuronal networks, and to still larger systems. it is backwards-compatible with GENESIS, and forward compatible with Python and XML-based model definition standards like SBML and MorphML. MOOSE is coordinating with the GENESIS-3 project towards the goals of developing educational resources for modeling. MOOSE is open source software, licensed under the LGPL (Lesser GNU Public License). It has absolutely no warranty. Sponsors: - National Center of Biological Sciences (NCBS) - National Institutes of Health (NIH) Collaboration - EU-India grid - Department of Atomic Energy Science Research Council (DAE/SRC) - Department of Biotechnology (DBT) | cell, computational, molecule, network, neuronal, neuroscience, simulation, subcellular, systems biology |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MUlti SImulation Coordinator has parent organization: SourceForge |
nif-0000-10307 | http://www.nitrc.org/projects/moose | SCR_008031 | MOOSE | 2026-02-15 09:19:41 | 302 | ||||||||
|
Diffusion Tensor Imaging ToolKit Resource Report Resource Website 10+ mentions |
Diffusion Tensor Imaging ToolKit (RRID:SCR_001642) | DTI-TK | software application, data processing software, software resource, image analysis software, software toolkit | A spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data with special care taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. A 2011 study published in NeuroImage ranks DTI-TK the top-performing tool in its class. Key features include: * open standard-based file IO support: NIfTI format for scalar, vector and tensor image volumes * tool chains for manipulating tensor image volumes: resampling, smoothing, warping, registration & visualization * pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies * built-in cluster-computing support: support for open source Sun Grid Engine (SGE) * Interoperability with other popular DTI tools: AFNI, Camino, FSL & DTIStudio * Interoperability with ITK-SNAP: support multi-modal visualization and segmentation | dti, visualization, segmentation, resampling, smoothing, warping, registration, spatial normalization, atlas construction, analysis, atlas application, intersubject, image-to-template, analyze, nifti-1, macos, linux |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion MRI of Traumatic Brain Injury is related to: Camino is related to: MRI Studio has parent organization: University of Pennsylvania; Philadelphia; USA has parent organization: SourceForge |
NIBIB 1R03EB009321-01 | Free, Available for download, Freely available | nlx_153914 | http://www.nitrc.org/projects/dtitk | SCR_001642 | 2026-02-15 09:18:08 | 22 | ||||||
|
openADAM Resource Report Resource Website |
openADAM (RRID:SCR_002018) | openADAM | data management software, software application, software resource | A web-based database management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Genome-Wide Human SNP Array platforms. | php, perl, front end, affymetrix genechip mapping array, affymetrix genome-wide human snp array, data management, affymetrix, snp, genome-wide association |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19117518 | Free, Available for download, Freely available | OMICS_01921 | SCR_002018 | 2026-02-15 09:18:13 | 0 | |||||||
|
SNVer Resource Report Resource Website 50+ mentions |
SNVer (RRID:SCR_002061) | software application, data processing software, data analysis software, software resource | Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data. | statistical analysis software, sequencing, dna, whole-exome, whole-genome, variant, bio.tools |
lists: SAMTOOLS is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:21813454 | Free, Available for download, Freely available | OMICS_00076, biotools:snver | https://sourceforge.net/projects/snver/ https://bio.tools/snver |
SCR_002061 | 2026-02-15 09:18:14 | 51 | |||||||
|
LIBEEP Resource Report Resource Website 1+ mentions |
LIBEEP (RRID:SCR_009591) | LIBEEP | software library, software toolkit, software resource | Software library that deals with reading and writing RIFF-format CNT/AVR-files. This file format is also called EEProbe data format, and is used in the software packages EEProbe, ASA, ASA-Lab, Cognitrace, eemagine EEG, Visor, by ANT Neuro B.V., The Netherlands. The file format provides for storage of EEG/ERP/MEG data as 32-bit values, and includes a very efficient compression algorithm. Encoding/decoding from the compressed data is performed automatically through the LIBEEP interface functions. | eeg, meg, electrocorticography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Libeep EEGLAB plugin has parent organization: SourceForge |
GNU Lesser General Public License, Plus Addendum | nlx_155781 | http://www.nitrc.org/projects/libeep | SCR_009591 | LIBEEP library | 2026-02-15 09:20:13 | 1 |
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.
