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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | standalone software, software resource, software application | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | ReadqPCR - Read qPCR data | 2026-08-07 09:24:55 | 0 | ||||||
|
mzMatch Resource Report Resource Website 1+ mentions |
mzMatch (RRID:SCR_000543) | software resource, software toolkit | 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 | 2026-08-07 09:25:02 | 5 | |||||||
|
Vascular Modeling Toolkit Resource Report Resource Website 50+ mentions |
Vascular Modeling Toolkit (RRID:SCR_001893) | vmtk | software toolkit, software resource, software application | Software collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels. | 3d reconstruction, geometric analysis, mesh generation, surface data analysis, image-based modeling, blood vessel, reconstruction, 3d |
is listed by: Debian is listed by: OMICtools is related to: VMTK in 3D Slicer |
PMID:19002516 PMID:19447701 DOI:10.1109/TMI.2009.2021652 |
Free, Available for download, Freely available | nlx_155869, OMICS_13947 | https://sources.debian.org/src/vmtk/ | SCR_001893 | vmtk - the Vascular Modeling Toolkit | 2026-08-07 09:25:19 | 99 | |||||
|
FLOSS Resource Report Resource Website |
FLOSS (RRID:SCR_000836) | FLOSS | software resource, software application | Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:floss, nlx_154319 | https://bio.tools/floss | SCR_000836 | FLexible Ordered SubSet analysis | 2026-08-07 09:25:05 | 0 | |||||||
|
DINDEL Resource Report Resource Website 10+ mentions |
DINDEL (RRID:SCR_001827) | Dindel | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems). | indel, short-read, next generation sequence, illumina, gene, genetic, genomic, c++, linux, macos, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:20980555 DOI:10.1101/gr.112326.110 |
THIS RESOURCE IS NO LONGER IN SERVICE | , nlx_154283, OMICS_00096, biotools:dindel | https://bio.tools/dindel, https://sources.debian.org/src/dindel/ | http://www.sanger.ac.uk/resources/software/dindel/ | SCR_001827 | Dindel: Accurate indel calls from short-read data | 2026-08-07 09:25:18 | 44 | ||||
|
metabnorm Resource Report Resource Website |
metabnorm (RRID:SCR_001266) | standalone software, software resource, software application | 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 ; Erik and Edith Fernström foundation ; Cancer Research UK |
PMID:24711654 | Free, Available for download, Freely available | OMICS_03548, biotools:metabnorm | https://bio.tools/metabnorm | SCR_001266 | 2026-08-07 09:25:11 | 0 | ||||||
|
PEDIGRAPH Resource Report Resource Website 10+ mentions |
PEDIGRAPH (RRID:SCR_001938) | Pedigraph | software resource, software application | A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles | gene, genetic, genomic, c, c++, ms-windows, linux, pedigree, java, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
PMID:14986440 | Acknowledgement required, Copyrighted | biotools:pedigraph, OMICS_00212, nlx_154519 | https://bio.tools/pedigraph | SCR_001938 | 2026-08-07 09:25:20 | 17 | ||||||
|
Apollo Resource Report Resource Website 100+ mentions |
Apollo (RRID:SCR_001936) | Apollo | software resource, software application | A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. | java, genome annotation, genome, annotation, windows, mac os x, linux, solaris, unix, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Generic Model Organism Database Project |
PMID:19439563 PMID:12537571 DOI:10.1186/gb-2002-3-12-research0082 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11761, biotools:apollo, OMICS_01933 | https://bio.tools/apollo, https://sources.debian.org/src/aragorn/ | SCR_001936 | 2026-08-07 09:25:19 | 301 | ||||||
|
lsa_slurm Resource Report Resource Website 1+ mentions |
lsa_slurm (RRID:SCR_018134) | software resource, source code | Software tool to implement pre-assembly binning scheme leveraging sparse dictionary learning and matrix factorization to solve sparse decomposition problems arising in field of metagenomics. | Sparse dictionary learning, pre-assembly binning scheme, matrix factorization, sparse decomposition, metagenomic, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:Metagenomic_read_binning_using_sparse_coding | https://bio.tools/Metagenomic_read_binning_using_sparse_coding | SCR_018134 | Metagenomic_read_binning_using_sparse_coding | 2026-08-07 09:28:55 | 1 | |||||||
|
C Thread Pool Resource Report Resource Website |
C Thread Pool (RRID:SCR_023999) | software resource, source code | Software for minimal but powerful thread pool in ANSI C. | thread pool, ANSI C, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/cthreadpool/ | SCR_023999 | C-Thread-Pool, cthreadpool | 2026-08-07 09:30:09 | 0 | ||||||||
|
sepp Resource Report Resource Website 1+ mentions |
sepp (RRID:SCR_024327) | software resource, source code | Ensemble of HMM methods.Repository includes code for SEPP, TIPP, UPP, HIPPI. Methods use ensembles of Hidden Markov Models in different ways, each focusing on different problem. | Ensemble of HMM methods, SEPP, TIPP, UPP, HIPPI, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/sepp/ | SCR_024327 | 2026-08-07 09:30:13 | 1 | |||||||||
|
EDFlib Resource Report Resource Website |
EDFlib (RRID:SCR_024010) | software resource, source code | Software programming library for C/C++ to read/write EDF+/BDF+ files.It also reads old-type EDF/BDF files. | programming library for C/C++, read/write EDF+/BDF+ files, EDF/BDF files, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/edflib/ | SCR_024010 | edflib | 2026-08-07 09:30:09 | 0 | ||||||||
|
Dicom3tools Resource Report Resource Website 1+ mentions |
Dicom3tools (RRID:SCR_024008) | software resource, source code | Software package provides DICOM medical image files manipulation and conversion tools. Command line utilities for creating, modifying, dumping and validating DICOM files. | DICOM medical image files, manipulation and conversion tools, creating DICOM files, modifying DICOM files, dumping DICOM files, validating DICOM files, | is listed by: Debian | Free, Freely available | https://sources.debian.org/src/dicom3tools/ | SCR_024008 | dicom3tools | 2026-08-07 09:30:09 | 2 | ||||||||
|
AxPcoords Resource Report Resource Website 1+ mentions |
AxPcoords (RRID:SCR_023971) | software resource, source code | Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Faster than DistPCoA and numerically stable on large datasets. | large scale co-phylogenetic analyses | is listed by: Debian | PMID:17953748 | Free, Available for download, Freely available | https://cme.h-its.org/exelixis/ | https://sources.debian.org/src/axpcoords/ | SCR_023971 | , axpcoords, Accelerated DistPCoA | 2026-08-07 09:30:02 | 1 | ||||||
|
AxParafit Resource Report Resource Website |
AxParafit (RRID:SCR_023968) | software resource, source code | Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Allows for rapid and much more thorough computation and analyses of large co-phylogenetic datasets. | large scale co-phylogenetic analyses, taxa, large co-phylogenetic datasets, co-phylogenetic datasets, | is listed by: Debian | PMID:17953748 | Free, Available for download, Freely available | https://sources.debian.org/src/axparafit/ | SCR_023968 | Accelerated Parafit, axparafit | 2026-08-07 09:30:02 | 0 | |||||||
|
Auspice Resource Report Resource Website 1+ mentions |
Auspice (RRID:SCR_023966) | software resource, source code | Web application for visualizing pathogen evolution.Interactive web app for visualizing phylogenomic data. | visualizing pathogen evolution, visualizing phylogenomic data, | is listed by: Debian | Free, Available for download, Freely available | https://docs.nextstrain.org/projects/auspice/en/stable/ | https://sources.debian.org/src/auspice/ | SCR_023966 | auspice | 2026-08-07 09:30:08 | 8 | |||||||
|
assembly-stats Resource Report Resource Website 50+ mentions |
assembly-stats (RRID:SCR_023963) | software resource, source code | Software to get assembly statistics from FASTA and FASTQ files. | assembly statistics, FASTA file, FASTQ files, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/assembly-stats/ | SCR_023963 | 2026-08-07 09:30:08 | 50 | |||||||||
|
DEXTRACTOR Resource Report Resource Website 1+ mentions |
DEXTRACTOR (RRID:SCR_024005) | software resource, source code | Software as Bax file decoder and data compressor. | Bax, file decoder, data compressor, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/dextractor/ | SCR_024005 | Dextractor and Compression Command Library, dextractor | 2026-08-07 09:30:02 | 2 | ||||||||
|
Java NeXML libraries and tools Resource Report Resource Website |
Java NeXML libraries and tools (RRID:SCR_024084) | software resource, source code | Software repository contains java code for NeXML processing. | Java code for NeXML processing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libnexml-java/ | SCR_024084 | nexml.java, libnexml-java | 2026-08-07 09:30:10 | 0 |
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.
