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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
qtlreaper Resource Report Resource Website |
qtlreaper (RRID:SCR_024199) | software application, data processing software, data analysis software, software resource | Software, written in C and compiled as Python module, for rapidly scanning microarray expression data for Quantitative Trait Locies. Searches for association between each expression trait and all genotypes and evaluates that association by permutation test. Performs bootstrap resampling to estimate confidence region for location of putative QTL. | rapidly scanning microarray expression data for QTLs, association between each expression trait and all genotypes, estimate confidence region for location of putative QTL, Quantitative Trait Loci, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/qtlreaper/ | SCR_024199 | 2026-02-15 09:23:25 | 0 | |||||||||
|
MHAP Resource Report Resource Website |
MHAP (RRID:SCR_024113) | software application, data processing software, data analysis software, software resource | Software tool as reference implementation of probabilistic sequence overlapping algorithm. Used to detect overlaps between noisy long-read sequence data. | detect overlaps between noisy long-read sequence data, probabilistic sequence overlapping algorithm, | is listed by: Debian | PMID:26006009 | Free, Available for download, Freely available, | OMICS_13515 | https://sources.debian.org/src/mhap/ https://github.com/marbl/MHAP |
SCR_024113 | MinHash Alignment Process, mhap | 2026-02-15 09:23:23 | 0 | ||||||
|
MindTheGap Resource Report Resource Website 1+ mentions |
MindTheGap (RRID:SCR_024115) | software application, data processing software, data analysis software, software resource | Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. | perform detection and assembly of DNA insertion variants, NGS read datasets, reference genome, call insertions, donor genome, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_05472 | https://sources.debian.org/src/mindthegap/ | SCR_024115 | mindthegap | 2026-02-15 09:23:33 | 3 | |||||||
|
MafFilter Resource Report Resource Website 10+ mentions |
MafFilter (RRID:SCR_024105) | software application, data processing software, data analysis software, software resource | Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc. | genome alignments analysis, parse and manipulate MAF files, genome alignment processor, | is listed by: Debian | PMID:24447531 | Free, Available for download, Freely available, | OMICS_06743 | https://sources.debian.org/src/maffilter/ https://github.com/jydu/maffilter |
SCR_024105 | MafFilter a genome alignment processor, maffilter | 2026-02-15 09:23:23 | 11 | ||||||
|
sparta Resource Report Resource Website 1+ mentions |
sparta (RRID:SCR_024349) | software application, data processing software, data analysis software, software resource | Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms. | analyzing single-end Illumina RNA-seq data, | is listed by: Debian | PMID:26847232 | Free, Available for download, Freely available, | https://sources.debian.org/src/sparta/ | SCR_024349 | SPARTA | 2026-02-15 09:23:27 | 9 | |||||||
|
Maude Resource Report Resource Website |
Maude (RRID:SCR_024108) | software library, portal, software resource, project portal, data or information resource, software toolkit | Software high performance reflective language and system supporting both equational and rewriting logic specification and programming for wide range of applications.Supports equational specification and programming, rewriting logic computation. | equational and rewriting logic specification and programming, equational specification and programming, rewriting logic computation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/maude/ http://maude.cs.illinois.edu/w/index.php/Maude_download_and_installation |
SCR_024108 | Maude, maude | 2026-02-15 09:22:36 | 0 | ||||||||
|
mPTP Resource Report Resource Website 1+ mentions |
mPTP (RRID:SCR_024121) | software application, data processing software, data analysis software, software resource | Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets. | single locus species delimitation, ML delimitation from inferred phylogenetic tree of the samples, ML delimitation, inferred phylogenetic tree, samples inferred phylogenetic tree, | is listed by: Debian | PMID:28108445 | Free, Available for download, Freely available, | OMICS_15264 | https://sources.debian.org/src/mptp/ | SCR_024121 | , mptp, multi-rate Poisson Tree Processes | 2026-02-15 09:23:23 | 1 | ||||||
|
Yanosim Resource Report Resource Website |
Yanosim (RRID:SCR_024363) | Yanosim | software application, simulation software, software resource | Software tool as read simulator for nanopore DRS datasets. | read simulator for nanopore DRS datasets, read simulator, nanopore DRS datasets, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/yanosim/ | SCR_024363 | yanosim, yet another nanopore simulator | 2026-02-15 09:23:41 | 0 | |||||||
|
Molekel Resource Report Resource Website 1+ mentions |
Molekel (RRID:SCR_024122) | software application, data visualization software, data processing software, software resource | Open source multi platform molecular visualization program. | molecular visualization | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/molekel/ | SCR_024122 | molekel | 2026-02-15 09:23:20 | 1 | ||||||||
|
MRtrix3 Resource Report Resource Website 100+ mentions |
MRtrix3 (RRID:SCR_024123) | software application, data processing software, data analysis software, software resource | Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses. | diffusion MRI analyses, tractography, next generation group level analyses, | is listed by: Debian | PMID:31473352 | Free, Available for download, Freely available, | https://sources.debian.org/src/mrtrix3/ | SCR_024123 | mrtrix3 | 2026-02-15 09:23:34 | 185 | |||||||
|
MIA Resource Report Resource Website |
MIA (RRID:SCR_024081) | software application, image analysis software, data processing software, software resource | Software toolkit for gray scale medical image analysis. Provides combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in command shell and prototype algorithms as shell scripts. MIA is build around a plug-in structure that makes it easy to add functionality without compromising the original code base, and it makes use of wide variety of external libraries that provide additional functionality. | gray scale medical image analysis, interactive image processing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/mia/ | https://sources.debian.org/src/libmialm/ | SCR_024081 | python3-mia, libmia-2.4-dev, mia-tools, mia-viewit, libvistaio-dev, libmialm-dev, libmiaviewit-dev, libmialm, mialmpick | 2026-02-15 09:23:22 | 0 | |||||||
|
SNPAAMapper Resource Report Resource Website |
SNPAAMapper (RRID:SCR_002012) | SNPAAMapper | software application, data processing software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5?UTR, etc). Major features: * The pipeline accepts the VCF (Variant Call Format) input file in tab-delimited format and processes the vcf input file containing all cases (G5, lowFreq, and novel) * The variant mapping step has the option of letting users select whether they want to report the bp distance between each identified intron variant and its nearby exon * The pipeline can deal with VCF files called by different SAMTools versions (0.1.18 and older ones) and also offers flexibility in dealing with vcf input files generated using SAMTools with two or three samples * The spreadsheet result file contains full protein sequences for both ref and alt alleles, which makes it easier for downstream protein structure/function analysis tools to take | single nucleotide polymorphism, amino acid, variant, annotation, exon, intron, mutation, next-generation sequencing, perl, downstream analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan Medical School; Michigan; USA |
PMID:24250114 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01922, biotools:snpaamapper | https://bio.tools/snpaamapper | SCR_002012 | SNPAAMapper - A SNP Amino Acid Mapping tool | 2026-02-15 09:18:13 | 0 | |||||
|
SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software toolkit, software resource | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-02-15 09:17:52 | 101 | |||
|
skewer Resource Report Resource Website 10+ mentions |
skewer (RRID:SCR_001151) | skewer | software application, data processing software, software resource | Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences. | illumina, unix/linux, c++, adapter trimming, paired-end, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24925680 | Free, Available for download, Freely available | OMICS_02106, biotools:skewer | https://bio.tools/skewer https://sources.debian.org/src/skewer/ https://github.com/relipmoc/skewer |
SCR_001151 | skewer - A fast and sensitive adapter trimmer for illumina paired-end sequences | 2026-02-15 09:18:03 | 11 | |||||
|
Mspire-Simulator Resource Report Resource Website 1+ mentions |
Mspire-Simulator (RRID:SCR_001431) | software application, simulation software, standalone software, software resource | A free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components. | standalone software, shotgun, proteomic, simulation software, bio.tools |
uses: mzML is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: Brigham Young University; Utah; USA |
PMID:24090032 | Free, Freely Available | biotools:mspire-simulator, OMICS_03359 | https://bio.tools/mspire-simulator | SCR_001431 | 2026-02-15 09:18:06 | 1 | |||||||
|
HTqPCR Resource Report Resource Website 50+ mentions |
HTqPCR (RRID:SCR_003375) | HTqPCR | software application, data processing software, software resource | Software package for the analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs). | data import, differential expression, gene expression, microtitre plate assay, multiple comparison, preprocessing, quality control, visualization, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
PMID:19808880 | Free, Available for download, Freely available | biotools:htqpcr, OMICS_02314 | https://bio.tools/htqpcr | SCR_003375 | HTqPCR - Automated analysis of high-throughput qPCR data | 2026-02-15 09:18:33 | 74 | |||||
|
NanoStringNorm Resource Report Resource Website 100+ mentions |
NanoStringNorm (RRID:SCR_003382) | NanoStringNorm | software application, data processing software, software resource | Software package for normalizing, diagnostics and visualization of NanoString nCounter data. Key features include an extensible environment for method comparison and new algorithm development, integrated gene and sample diagnostics, and facilitated downstream statistical analysis. | normalization, nanostring ncounter, mirna, mrna, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Ontario Institute for Cancer Research |
PMID:22513995 | Free, Available for download, Freely available | OMICS_02308, biotools:nanostringnorm | https://www.rdocumentation.org/packages/NanoStringNorm/versions/1.2.1.1/topics/NanoStringNorm | SCR_003382 | NanoStringNorm: Normalize NanoString miRNA and mRNA data | 2026-02-15 09:18:30 | 134 | |||||
|
University of Zurich SCRM - Cell-and Tissue Biobank Resource Report Resource Website |
University of Zurich SCRM - Cell-and Tissue Biobank (RRID:SCR_004959) | SCRM-CTBB | material resource, cell repository, biomaterial supply resource | The SCRM-CTBB offers state-of-the-art infrastructure and technologies (e.g. cryogenic work bench, semiautomatic cryogenic storage system, uninterrupted cooling chain) and is structured into two areas, including research and a GMP/GCP regulated therapeutic applications. Research: For pre-clinical studies, the SCRM-CTBB provides researchers guidance regarding cell and tissue cryo-preservation, comprising registration, handling, storage and distribution. In order to ensure complete traceability on samples and belonging information all processes are controlled by a Laboratory Information Management System (LIMS) and Quality Assurance (QA) system. The SCRM Biobank is designed to create database that allows connection with other biobanks nationally and internationally. This meta-data file will enable a unique scientific resource for interdisciplinary research. For every new study a contract is established describing the study and the disposition rights. Assistance in writing Biobank Agreements (BAs) and Material Transfer Agreements (MTAs) is provided. Therapeutical applications: As a new feature, apart from research, the SCRM Biobank enables the asservation and preservation of cells and tissues under GMP conditions for later therapeutic use. A special focus will be on a conceptional combination of private and public umbilical cord blood banking (hybrid banking), which allows autologous and/or allogeneic cell applications. | cell, tissue, umbilical cord blood, blood, cryopreserved, therapy, research, clinical, frozen, transplantation |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: OMICtools has parent organization: University of Zurich; Zurich; Switzerland |
Public: The SCRM Biobank is designed to create database that allows connection with other biobanks nationally and internationally. This meta-data file will enable a unique scientific resource for interdisciplinary research. | nlx_143985, OMICS_07231 | https://sources.debian.org/src/scrm/ | SCR_004959 | University of Zurich SCRM - Cell Tissue Biobank, UZH Swiss Center for Regenerative Medicine Cell-and Tissue Biobank, University of Zurich SCRM - Cell and Tissue Biobank, UZH SCRM-CTBB, SCRM Biobank, SCRM - Cell-and Tissue Biobank (CTBB), University of Zurich Swiss Center for Regenerative Medicine Cell-and Tissue Biobank, UZH SCRM - Cell-and Tissue Biobank, SCRM - Cell- Tissue Biobank | 2026-02-15 09:18:58 | 0 | ||||||
|
PEPPER Resource Report Resource Website 1+ mentions |
PEPPER (RRID:SCR_000431) | PEPPER | software application, software resource | A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...). | plugin, protein-protein interaction, network, bio.tools |
is listed by: OMICtools is listed by: Cytoscape is listed by: bio.tools is listed by: Debian |
PMID:25138169 | Free, Available for download, Freely available | biotools:pepper, OMICS_05485 | https://bio.tools/pepper | SCR_000431 | Protein complex Expansion using Protein-Protein intERaction networks, Protein complex Expansion using Protein-Protein intERactions | 2026-02-15 09:17:55 | 1 | |||||
|
dinifti Resource Report Resource Website 1+ mentions |
dinifti (RRID:SCR_000303) | dinifti | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software which converts DICOM images to NIfTI format. | analyze, console (text based), dicom, format conversion, freebsd, linux, magnetic resonance, nifti, posix/unix-like |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: New York University; New York; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155843 | http://www.nitrc.org/projects/dinifti http://cbi.nyu.edu/software/dinifti.php https://sources.debian.org/src/dicomnifti/ |
SCR_000303 | NYU CBI DICOM to NIfTI Converter | 2026-02-15 09:17:54 | 2 |
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.
