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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | TARQUIN MRS analysis package | 2026-02-15 09:18:21 | 58 | |||||
|
VARSCAN Resource Report Resource Website 1000+ mentions |
VARSCAN (RRID:SCR_006849) | VarScan | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, java, illumina, solid, life/pgm, roche/454, next-generation sequencing, variant, mutation caller, exome, whole-genome, snp, copy number alteration, somatic mutation, subclonal mutation, mutation, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:22300766 PMID:19542151 DOI:10.1101/gr.129684.111 |
THIS RESOURCE IS NO LONGER IN SERVICE | , nlx_154687, biotools:varscan, OMICS_00094 | http://varscan.sourceforge.net/ http://dkoboldt.github.io/varscan/ https://bio.tools/varscan https://sources.debian.org/src/varscan/ |
http://genome.wustl.edu/software/varscan | SCR_006849 | Varscan2, VarScan - variant detection in massively parallel sequencing data, Varscan | 2026-02-15 09:19:20 | 1769 | ||||
|
HTQC Resource Report Resource Website 10+ mentions |
HTQC (RRID:SCR_006448) | HTQC | software toolkit, software resource | 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 | HTQC - Quality control and filtration for illumina sequencing data | 2026-02-15 09:19:17 | 42 | |||||
|
GeneVenn Resource Report Resource Website 100+ mentions |
GeneVenn (RRID:SCR_012117) | service resource, analysis service resource, data analysis service, production service resource | A web application creating Venn diagrams from two or three gene lists. | web app |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:17597932 | OMICS_05568 | SCR_012117 | 2026-02-15 09:20:26 | 101 | |||||||||
|
PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software application, software resource | A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | 2026-02-15 09:17:58 | 0 | ||||||
|
Magnolya Resource Report Resource Website 1+ mentions |
Magnolya (RRID:SCR_000164) | software application, data analytics software, software resource | A software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets. | algorithm, copy number, next-generation, reference genome, dataset comparison |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23047563 | Free, Available for download, Freely available | OMICS_00347 | SCR_000164 | 2026-02-15 09:17:52 | 2 | ||||||||
|
UTR Resource Report Resource Website |
UTR (RRID:SCR_000045) | software application, standalone software, software resource | Software application that uses change point model for detecting 3-prime UTR changes by RNA-Seq. | java, 3 prime utr, rna sequence, change point model, detecting 3-prime UTR changes, RNA-Seq |
uses: R Project for Statistical Computing has parent organization: SourceForge |
PMID:24728858 | Free, Available for download, Freely available | OMICS_04052 | SCR_000045 | 2026-02-15 09:17:51 | 0 | ||||||||
|
mzMatch Resource Report Resource Website 1+ mentions |
mzMatch (RRID:SCR_000543) | software toolkit, software resource | A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java. | metabolomics, analysis, java, tool, peak extraction, filtering, normalization, derivative detection, identification, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23162054 | Free, Available for download, Freely available, | biotools:mzmatch, OMICS_02642 | https://bio.tools/mzmatch | SCR_000543 | 2026-02-15 09:17:56 | 5 | |||||||
|
Hanalyzer Resource Report Resource Website |
Hanalyzer (RRID:SCR_000923) | software application, source code, software resource | An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download. | genomic, visualization, reading, reasoning, reporting, throughput analyzer, data network |
has parent organization: University of Colorado Denver; Colorado; USA has parent organization: SourceForge |
NIDCR R01DE15191; NLM R01LM008111; NLM R01LM009254; NIGMS R01GM083649; NLM T15LM009451; NHGRI 5R01HG004483-09 |
PMID:19325874 | nlx_48287 | SCR_000923 | Hanalyzer: A 3R System | 2026-02-15 09:18:01 | 0 | |||||||
|
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 | |||||||
|
RUbioSeq Resource Report Resource Website 10+ mentions |
RUbioSeq (RRID:SCR_002508) | software application, sequence analysis software, data processing software, software resource, standalone software, data analysis software | Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments. | resequencing analysis, exome variant detection, pipeline, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
BLUEPRINT Consortium FP7/2007-2013 282510; Spanish Ministry of Economy and Competitiveness BIO2007-666855 |
PMID:23630175 | Free, Available for download | biotools:rubioseq, OMICS_00072 | https://sourceforge.net/projects/rubioseq/files/ https://bio.tools/rubioseq |
SCR_002508 | RUbioSeq+ | 2026-02-15 09:18:19 | 12 | |||||
|
ViReMa Resource Report Resource Website 1+ mentions |
ViReMa (RRID:SCR_000566) | ViReMa | software application, data processing software, software resource, software toolkit, data analysis software | Software Python package for detection, alignment and reporting of recombination events in Next-Generation Sequencing data. Detects and reports recombination or fusion events in virus genomes using deep sequencing datasets. | virus genomes deep sequencing datasets, detection, alignment and reporting of recombination events, Next-Generation Sequencing data, |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Scripps Research Institute |
PMID:24137010 | Free, Available for download, Freely available, | OMICS_00225 | SCR_000566 | Viral Recombination Mapper | 2026-02-15 09:17:57 | 2 | ||||||
|
SparseAssembler Resource Report Resource Website 1+ mentions |
SparseAssembler (RRID:SCR_001100) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software for memory-efficient genome assembly. It utilizes sparse k-mer. | genome, genomics, genome assembly, k-mer, sequence analysis software, memory |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22537038 | Free, Available for download, Freely available | OMICS_00032 | SCR_001100 | 2026-02-15 09:18:02 | 1 | ||||||||
|
ChIP-seq Resource Report Resource Website 5000+ mentions |
ChIP-seq (RRID:SCR_001237) | ChIP-seq | software application, data processing software, software resource, software toolkit, data analysis software | Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface. | high-throughput sequencing, chromatin immuno precipitation, chip-seq, genome, c |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:27863463 | Free, Available for download, Freely available | OMICS_02103 | https://epd.expasy.org/chipseq/ https://chip-seq.sourceforge.net/ |
SCR_001237 | ChIP-seq - Tools for the analysis of ChIP-seq data | 2026-02-15 09:18:04 | 7500 | |||||
|
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 | ||||||
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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 | ||||||
|
Wisconsin White Matter Hyperintensities Segmentation Toolbox Resource Report Resource Website 1+ mentions |
Wisconsin White Matter Hyperintensities Segmentation Toolbox (RRID:SCR_009652) | W2MHS | software application, software library, data processing software, software resource, segmentation software, image analysis software, software toolkit | An open source MATLAB toolbox designed for detecting and quantifying White Matter Hyperintensities(WMH) in Alzheimer?s and aging related neurological disorders.Our toolbox provides a self-sufficient set of tools for segmenting these WMHs reliably and further quantifying their burden for down-processing studies. WMHs arise as bright regions on T2-weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden. Their precise detection is of interest in Alzheimer?s disease (AD) with regard to its prognosis. | computational neuroscience, matlab, nifti, white matter hyperintensity, c++, matlab, ms windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM is related to: SourceForge has parent organization: University of Wisconsin-Madison; Wisconsin; USA has parent organization: SourceForge |
Alzheimer's disease, Aging, Neurological disorder | Academic Free License | nlx_156021 | SCR_009652 | WM Hyperintensities Segmentation Toolbox | 2026-02-15 09:19:47 | 1 | ||||||
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CPFP Resource Report Resource Website 1+ mentions |
CPFP (RRID:SCR_012043) | software application, data processing software, data analysis software, software resource | Software providing a data analysis pipeline for shotgun mass-spectrometry proteomics. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: University of Oxford; Oxford; United Kingdom |
PMID:20189941 | OMICS_02448, biotools:cpfp | https://bio.tools/cpfp | SCR_012043 | Central Proteomics Facilities Pipeline | 2026-02-15 09:20:08 | 7 | |||||||
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Bionotate Resource Report Resource Website 1+ mentions |
Bionotate (RRID:SCR_012098) | data analysis service, software resource, service resource, production service resource, analysis service resource | An open source annotation tool for the distributed creation of a large corpus. | web app |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19232400 | GNU General Public License | OMICS_05229 | SCR_012098 | 2026-02-15 09:20:26 | 1 |
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