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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
BEDTools Resource Report Resource Website 10000+ mentions |
BEDTools (RRID:SCR_006646) | BEDTools | software resource | A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line. | genomics, bed, sam, bam, overlap, sequencing, intersect, coverage, gff, vcf, bedgraph, interval, genome arithmetic, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Hydra is related to: pybedtools is required by: SL-quant |
PMID:20110278 DOI:10.1093/bioinformatics/btq033 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01159, biotools:bedtools | https://code.google.com/p/bedtools/, https://bio.tools/bedtools, https://sources.debian.org/src/bedtools/ | SCR_006646 | bedtools - a swiss army knife for genome arithmetic, bedtools: a flexible suite of utilities for comparing genomic features | 2026-08-01 12:03:11 | 10394 | |||||
|
caftools Resource Report Resource Website |
caftools (RRID:SCR_023982) | software resource | Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site. | is listed by: Debian | Free, Available for download, Freely available | OMICS_24974 | https://sources.debian.org/src/caftools/ | SCR_023982 | 2026-08-01 12:08:24 | 0 | |||||||||
|
Conquest DICOM Resource Report Resource Website |
Conquest DICOM (RRID:SCR_023993) | softwre application | Software for DICOM training and testing,Demonstration and research image archives,Image format conversion from scanner with DICOM network access,DICOM image viewing and slide making, DICOM image selection, (limited) editing, and splitting and merging of series, Advanced scriptable image modification, filtering, forwarding and conversion, DICOM caching and archive merging, DICOM web access for viewing and data management (scriptable),Connection to Lua IDE for all sorts of DICOM manipulation. | DICOM training and testing, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/conquest/ | SCR_023993 | conquest-common, conquest-dbase, conquest-postgres, conquest-dicom-server, conquest-sqlite, conquest-mysql | 2026-08-01 12:07:59 | 0 | ||||||||
|
CHIME Resource Report Resource Website |
CHIME (RRID:SCR_023987) | softwre application | Software designed to assist hospitals and public health officials with understanding hospital capacity needs as they relate to the COVID pandemic. CHIME enables capacity planning by providing estimates of total daily and running totals of inpatient hospitalizations, ICU admissions, and patients requiring ventilation. | providing estimates, capacity planning, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/chime/ | SCR_023987 | COVID-19 Hospital Impact Model for Epidemics, chime | 2026-08-01 12:08:13 | 0 | ||||||||
|
EMMAX Resource Report Resource Website 1+ mentions |
EMMAX (RRID:SCR_024012) | softwre application | Software statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model. | statistical test, human or model organism association mapping, sample structure, association mapping | is listed by: Debian | Free, Available for download, Freely available | OMICS_08871 | https://sources.debian.org/src/emmax/ | SCR_024012 | Efficient Mixed-Model Association eXpedited, emmax | 2026-08-01 12:07:59 | 3 | |||||||
|
dicompyler Resource Report Resource Website |
dicompyler (RRID:SCR_024006) | softwre application | Software extensible open source radiation therapy research platform based on the DICOM standard. It also functions as a cross-platform DICOM RT viewer. | radiation therapy research platform, DICOM standard, cross platform DICOM RT viewer, | is listed by: Debian | DOI:10.1118/1.3468652 | Free, Available for download, Freely available | https://sources.debian.org/src/dicompyler/, https://github.com/bastula/dicompyler | SCR_024006 | 2026-08-01 12:08:24 | 0 | ||||||||
|
foreign Resource Report Resource Website |
foreign (RRID:SCR_024025) | softwre application | Software tool for reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files. | Reading and writing data, 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', reading and writing some 'dBase' files, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/foreign/ | SCR_024025 | r-cran-foreign | 2026-08-01 12:08:24 | 0 | ||||||||
|
Deepbinner Resource Report Resource Website |
Deepbinner (RRID:SCR_024001) | softwre application | Software tool for demultiplexing barcoded Oxford Nanopore sequencing reads.Signal level demultiplexer for Oxford Nanopore reads. | signal level demultiplexer, Oxford Nanopore reads, demultiplexing barcoded Oxford Nanopore sequencing reads, | is listed by: Debian | PMID:30458005 | Free, Available for download, Freely available | OMICS_30643 | https://sources.debian.org/src/deepbinner/ | SCR_024001 | deepbinner | 2026-08-01 12:08:14 | 0 | ||||||
|
VennDiagram Resource Report Resource Website 1000+ mentions |
VennDiagram (RRID:SCR_002414) | software toolkit, software resource | Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure. | Venn and Euler plots, mac os x, unix/linux, windows, r |
is listed by: OMICtools is listed by: Debian is related to: jVenn has parent organization: CRAN |
PMID:21269502 | Free, Available for download, Freely available | OMICS_05570 | https://sources.debian.org/src/r-cran-venndiagram/ | SCR_002414 | VennDiagram: Generate high-resolution Venn and Euler plots | 2026-08-02 09:03:31 | 1811 | ||||||
|
MAKER Resource Report Resource Website 1000+ mentions |
MAKER (RRID:SCR_005309) | software toolkit, software resource | Software genome annotation pipeline. Portable and easily configurable genome annotation pipeline. Used to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence based quality values. | gene prediction, genome annotation, identifies repeats, aligns ESTs and proteins to genome, data management, genome annotation, annotation, curation, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: MAKER Web Annotation Service has parent organization: University of Utah; Utah; USA |
PMID:25501943 | SCR_023883, nlx_144363, biotools:maker | https://bio.tools/maker, https://github.com/Yandell-Lab/maker | SCR_005309 | Maker2, maker | 2026-08-02 09:04:17 | 1422 | |||||||
|
Eigensoft Resource Report Resource Website 1000+ mentions Issue |
Eigensoft (RRID:SCR_004965) | EIGENSOFT | software toolkit, software resource | EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction. | population genetics, genetics, stratification, variation |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: Harvard Medical School; Massachusetts; USA |
PMID:17194218 DOI:10.1038/ng1847 |
OMICS_07868, nlx_93059 | https://sources.debian.org/src/eigensoft/ | http://genepath.med.harvard.edu/~reich/Software.htm | SCR_004965 | EIGENSOFT Software | 2026-08-02 09:04:06 | 1225 | |||||
|
Unipro UGENE Resource Report Resource Website 100+ mentions |
Unipro UGENE (RRID:SCR_005579) | UGENE | software toolkit, software resource | A multiplatform open-source software to assist molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. | c++, windows, mac os, linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22368248 DOI:10.1093/bioinformatics/bts091 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01022, biotools:ugene | https://bio.tools/ugene, https://sources.debian.org/src/ugene/ | SCR_005579 | 2026-08-02 09:04:16 | 170 | ||||||
|
pydicom Resource Report Resource Website 50+ mentions |
pydicom (RRID:SCR_002573) | pydicom | software toolkit, software resource | Software Python package for working with DICOM files, made for inspecting and modifying DICOM data in an easy pythonic way. The modifications can be written again to a new file. As a pure python package, it should run anywhere python runs without any other requirements. | reusable library, console (text based), dicom, magnetic resonance, os independent, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian |
Free, Available for download, Freely available | nlx_155976 | http://www.nitrc.org/projects/pydicom, https://sources.debian.org/src/python3-pydicom/, | http://pydicom.googlecode.com | SCR_002573 | 2026-08-02 09:03:38 | 90 | ||||||
|
NGSUtils Resource Report Resource Website 10+ mentions |
NGSUtils (RRID:SCR_001236) | NGSUtils | software toolkit, software resource | A suite of software tools for analyzing and manipulating next-generation sequencing datasets, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis. | mac os x, linux, next-generation sequencing, illumia, solid, 454, ion torrent, pac bio, sequencing, dna resequcing, rna resequcing, chip-seq, clip-seq, targeted resequencing, agilent exome capture, pcr targeting, dna, rna, mapping pipeline, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Indiana University School of Medicine; Indiana; USA |
PMID:23314324 | Free, Available for download, Freely available | biotools:ngsutils, OMICS_02104 | https://bio.tools/ngsutils | SCR_001236 | NGSUtils - Tools for next-generation sequencing analysis | 2026-08-02 09:03:04 | 38 | |||||
|
khmer Resource Report Resource Website 10+ mentions |
khmer (RRID:SCR_001156) | software toolkit, software resource | Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. | dna sequence, short-read, sequencing, dna, illumina, sequence analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01HG007513 | PMID:26535114 DOI:10.12688/f1000research.6924.1 |
Free, Available for download, Freely available | SciRes_000166, OMICS_02560, biotools:khmer | https://github.com/dib-lab/khmer, https://bio.tools/khmer, https://sources.debian.org/src/khmer/ | https://github.com/ged-lab/khmer, http://ged.msu.edu/papers/2012-diginorm/ | SCR_001156 | khmer project, khmer - k-mer counting & filtering FTW, khmer - k-mer counting and filtering FTW, khmer: k-mer counting filtering and graph traversal FTW | 2026-08-02 09:03:00 | 25 | ||||
|
pRESTO Resource Report Resource Website 50+ mentions |
pRESTO (RRID:SCR_001782) | pRESTO | software toolkit, software resource | Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. | lymphocyte, high throughput sequencing, processing, raw reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale School of Medicine; Connecticut; USA |
EMD/Merck/Serono ; United States-Israel Binational Science Foundation 2009046; NCRR RR19895; NLM T15 LM07056; NIAAA U19AI089992; NIAAA U19AI050864 |
PMID:24618469 | Free, Freely available | SCR_001782 | REpertoire Sequencing TOolkit | 2026-08-02 09:03:16 | 70 | ||||||
|
RDKit: Open-Source Cheminformatics Software Resource Report Resource Website 100+ mentions |
RDKit: Open-Source Cheminformatics Software (RRID:SCR_014274) | software toolkit, software resource | An open-source cheminformatics and machine-learning toolkit that is useable from Java or Python. It includes a collection of standard cheminformatics functionality for molecule I/O, substructure searching, chemical reactions, coordinate generation (2D or 3D), fingerprinting, etc., as well as a high-performance database cartridge for working with molecules using the PostgreSQL database. Documentation is available on the main website. | cheminformatics, machine learning, software toolkit, open source, python, c++, FASEB list |
is listed by: Debian is listed by: OMICtools |
Open source, Acknowledgement requested | OMICS_14853 | https://github.com/rdkit https://sourceforge.net/projects/rdkit/ | https://sources.debian.org/src/python3-rdkit/ | SCR_014274 | RDKit, RDKit Open-Source Cheminformatics and Machine Learning | 2026-08-02 09:06:30 | 465 | ||||||
|
Cluster Resource Report Resource Website 5000+ mentions |
Cluster (RRID:SCR_013505) | Cluster | software toolkit, software resource | Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets. | Cluster analysis, processing on large microarray datasets |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
PMID:14871861 | Free, Available for download, Freely available | OMICS_01571 | http://www.eisenlab.org/eisen/?page_id=42, https://sources.debian.org/src/cluster3/ | SCR_013505 | Cluster 3.0 | 2026-08-02 09:06:17 | 5669 | |||||
|
DCMTK: DICOM Toolkit Resource Report Resource Website 10+ mentions |
DCMTK: DICOM Toolkit (RRID:SCR_007360) | software toolkit, software resource | Software collection of libraries and applications implementing large parts of DICOM standard for medical image communication.Includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over network connection, as well as demonstrative image storage and worklist servers. | is listed by: Debian | Free, Freely available | nif-0000-00283 | https://sources.debian.org/src/dcmtk/ | SCR_007360 | DCMTK | 2026-08-02 09:05:05 | 13 | ||||||||
|
Ghemical Resource Report Resource Website 10+ mentions |
Ghemical (RRID:SCR_014899) | software toolkit, software resource | Molecular modelling software package with 3D-visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). It contains geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms. | molecular modeling, 3d visualization, molecular mechanics, quantum mechanics, geometry organization, molecular dynamics |
is listed by: Debian is listed by: OMICtools |
Available for download | OMICS_21304 | https://sources.debian.org/src/ghemical/ | https://www.uku.fi/~thassine/projects/ghemical | SCR_014899 | 2026-08-02 09:06:41 | 18 |
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.
