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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MatNMR Resource Report Resource Website 10+ mentions |
MatNMR (RRID:SCR_012060) | software resource | A highly flexible software toolbox for processing 1D and 2D NMR and EPR spectra under MATLAB, creating high-quality 1D, 2D or 3D plots from the spectra and printing them in every type of format that is supported by MATLAB. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17448713 | OMICS_03375 | SCR_012060 | 2026-02-07 02:08:22 | 16 | |||||||||
|
GenoTan Resource Report Resource Website 1+ mentions |
GenoTan (RRID:SCR_007935) | GenoTan | software resource | A free software tool to identify length variation of microsatellites from short sequence reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24135263 | GNU General Public License, v3 | biotools:genotan | https://bio.tools/genotan | SCR_007935 | GenoTan - Genotyping of microsatellite loci | 2026-02-07 02:07:41 | 1 | |||||
|
BRIG Resource Report Resource Website 100+ mentions |
BRIG (RRID:SCR_007802) | BRIG | software resource | A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.1186/1471-2164-12-402 | OMICS_00929, biotools:brig | https://bio.tools/brig https://sources.debian.org/src/brig/ |
SCR_007802 | BLAST Ring Image Generator | 2026-02-07 02:07:41 | 491 | ||||||
|
SeqPig Resource Report Resource Website 1+ mentions |
SeqPig (RRID:SCR_008548) | SeqPig | software resource | A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters. | mapreduce/hadoop |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24149054 | OMICS_01226 | SCR_008548 | 2026-02-07 02:07:29 | 2 | ||||||||
|
GLProbs Resource Report Resource Website 1+ mentions |
GLProbs (RRID:SCR_002739) | software resource | Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:26357079 | Free, Freely available, Available for download | OMICS_03732 | SCR_002739 | 2026-02-07 02:05:49 | 1 | ||||||||
|
rDock Resource Report Resource Website 100+ mentions |
rDock (RRID:SCR_002838) | software resource | A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24722481 | Free, Freely available, Available for download | OMICS_03835 | SCR_002838 | 2026-02-07 02:05:51 | 107 | ||||||||
|
CONTRA Resource Report Resource Website 100+ mentions |
CONTRA (RRID:SCR_010814) | CONTRA | software resource | A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_00331, biotools:contra | https://bio.tools/contra | SCR_010814 | 2026-02-07 02:08:02 | 280 | ||||||||
|
SVDetect Resource Report Resource Website 10+ mentions |
SVDetect (RRID:SCR_010812) | SVDetect | software resource | Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads. | structural variation, sequencing, chromosomal rearrangement, high-throughput sequencing, solid, illumina, genome, insertion, deletion, inversion, duplication, translocation, command-line, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Curie Institute; Paris; France |
PMID:20639544 | GNU General Public License, v3 | OMICS_00324, biotools:svdetect | https://bio.tools/svdetect | SCR_010812 | SVDetect: a tool to detect genomic structural variations from paired-end and mate-pair sequencing data | 2026-02-07 02:07:53 | 22 | |||||
|
Celera assembler Resource Report Resource Website 50+ mentions |
Celera assembler (RRID:SCR_010750) | Celera assembler | software resource | A de novo whole-genome shotgun (WGS) DNA sequence assembler. |
is listed by: OMICtools is related to: Canu has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00009 | SCR_010750 | 2026-02-07 02:08:00 | 56 | |||||||||
|
FindPeaks Resource Report Resource Website 100+ mentions |
FindPeaks (RRID:SCR_010857) | FindPeaks | software resource | Software application that can be used for converting Eland, Maq (.map), BED or other files into WIG files and identifying areas of enrichment (ChIP-Seq analysis). | chip-seq |
is listed by: OMICtools has parent organization: SourceForge |
BC Cancer Agency ; Michael Smith Foundation for Health Research |
OMICS_00440 | SCR_010857 | 2026-02-07 02:08:03 | 317 | ||||||||
|
Genovar Resource Report Resource Website 1+ mentions |
Genovar (RRID:SCR_010930) | Genovar | software resource | A Detection and Visualization software tool for Genomic Variants. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Korea National Institute of Health |
Free, Public | OMICS_00724, biottools:genovar | https://bio.tools/genovar | SCR_010930 | 2026-02-07 02:08:07 | 1 | |||||||
|
PeakRanger Resource Report Resource Website 10+ mentions |
PeakRanger (RRID:SCR_010863) | PeakRanger | software resource | Software for a multi-purpose ChIP Seq peak caller. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21554709 | OMICS_00451, biotools:peakranger | https://bio.tools/peakranger | SCR_010863 | 2026-02-07 02:07:54 | 21 | |||||||
|
SEAL Resource Report Resource Website 100+ mentions |
SEAL (RRID:SCR_010914) | SEAL | software resource | A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21697132 | biotools:seal, OMICS_00682 | https://bio.tools/seal | SCR_010914 | 2026-02-07 02:07:55 | 119 | |||||||
|
CloudBurst Resource Report Resource Website |
CloudBurst (RRID:SCR_010911) | CloudBurst | software resource | A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19357099 | Free | OMICS_00657, biotools:cloudburst | https://bio.tools/cloudburst | SCR_010911 | 2026-02-07 02:08:04 | 0 | ||||||
|
ERNE Resource Report Resource Website 10+ mentions |
ERNE (RRID:SCR_010912) | ERNE | software resource | A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00662 | SCR_010912 | 2026-02-07 02:07:55 | 43 | ||||||||||
|
DNPTrapper Resource Report Resource Website |
DNPTrapper (RRID:SCR_010981) | DNPTrapper | software resource | An assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:16549006 | OMICS_00881 | SCR_010981 | 2026-02-07 02:08:08 | 0 | ||||||||
|
Hawkeye Resource Report Resource Website 1+ mentions |
Hawkeye (RRID:SCR_010982) | Hawkeye | software resource | A visual analytics tool for genome assembly analysis and validation, designed to aid in identifying and correcting assembly errors. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00884 | SCR_010982 | 2026-02-07 02:08:05 | 9 | ||||||||||
|
MZmine Resource Report Resource Website 500+ mentions |
MZmine (RRID:SCR_012040) | software resource | Software for mass-spectrometry data processing, with the main focus on LC-MS data. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20650010 | Open unspecified license | OMICS_02385 | SCR_012040 | 2026-02-07 02:08:29 | 788 | ||||||||
|
ORCA Resource Report Resource Website 1000+ mentions |
ORCA (RRID:SCR_012097) | software resource | A Matlab package extending the scope of established COBRA metabolic modelling. | software package, matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24336807 | Free for academic use | OMICS_05191 | SCR_012097 | 2026-02-07 02:08:28 | 1227 | ||||||||
|
COBRApy Resource Report Resource Website 100+ mentions |
COBRApy (RRID:SCR_012096) | software resource | Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods. | software package, mac os x, unix/linux, windows, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23927696 DOI:10.1186/1752-0509-7-74 |
OMICS_05190, biotools:cobrapy | https://bio.tools/cobrapy | https://sources.debian.org/src/python3-cobra/ | SCR_012096 | COBRA for Python | 2026-02-07 02:08:23 | 293 |
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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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 dkNET 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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
Email: info_at_ dknet.org
