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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ExpressionView Resource Report Resource Website |
ExpressionView (RRID:SCR_012004) | ExpressionView | software resource | An R package that provides an interactive environment to explore biclusters identified in gene expression data. | is listed by: OMICtools | PMID:20671149 | Free | OMICS_01800 | SCR_012004 | ExpressionView - Visualize biclusters identified in gene expression data | 2026-08-08 11:59:56 | 0 | |||||||
|
BiBench Resource Report Resource Website |
BiBench (RRID:SCR_012003) | BiBench | software resource | A Python library designed to simplify biclustering tasks. | is listed by: OMICtools | OMICS_01798 | SCR_012003 | 2026-08-08 11:59:38 | 0 | ||||||||||
|
AACC Resource Report Resource Website 100+ mentions |
AACC (RRID:SCR_011999) | AACC | data or information resource, portal, community building portal | An international society comprised of medical professionals with an interest in clinical chemistry, clinical laboratory science, and laboratory medicine. | is listed by: OMICtools | OMICS_01788 | SCR_011999 | American Association for Clinical Chemistry | 2026-08-08 11:59:38 | 264 | |||||||||
|
Pride-asap Resource Report Resource Website 10+ mentions |
Pride-asap (RRID:SCR_012052) | software resource | An open source software application and library written in Java that provides a uniform annotation of identified spectra stored in the PRIDE database. | standalone software, java |
is listed by: OMICtools has parent organization: Google Code |
PMID:23603108 | OMICS_03348 | SCR_012052 | 2026-08-08 11:59:39 | 10 | |||||||||
|
XTandem Parser Resource Report Resource Website |
XTandem Parser (RRID:SCR_012055) | software resource | An open-source Java library that parses X!Tandem XML result files into an easily accessible and fully functional object model. | standalone software, java |
is listed by: OMICtools is related to: X!Tandem is related to: X!Tandem has parent organization: Google Code |
PMID:20140905 | Apache License | OMICS_03353 | SCR_012055 | 2026-08-08 11:59:39 | 0 | ||||||||
|
Maltcms Resource Report Resource Website |
Maltcms (RRID:SCR_012057) | software resource | An application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_03356 | SCR_012057 | Modular Application Toolkit for Chromatography Mass-Spectrometry | 2026-08-08 12:00:05 | 0 | ||||||||||
|
PRIDE Converter 2 Resource Report Resource Website 1+ mentions |
PRIDE Converter 2 (RRID:SCR_012051) | software resource | Suite of software tools that allows users to convert search result files into PRIDE XML, generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra. | standalone software, mac os x, unix/linux, windows, java, xml, mass spectrometry, pride, ols, proteomics, psi, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Google Code |
PMID:22949509 | Apache License, v2 | biotools:pride_converter, OMICS_03344 | https://bio.tools/pride_converter | SCR_012051 | PRIDE, PRoteomics IDEntification (PRIDE) Converter 2 | 2026-08-08 12:00:05 | 1 | ||||||
|
jmzReader Resource Report Resource Website 1+ mentions |
jmzReader (RRID:SCR_012050) | software resource | A collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML. | standalone software, mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: Google Code |
PMID:22539430 | Apache License | OMICS_03341 | SCR_012050 | 2026-08-08 11:59:56 | 2 | ||||||||
|
FIGG Resource Report Resource Website 1+ mentions |
FIGG (RRID:SCR_012064) | software resource | A large-scale whole genome simulation tool which generates large numbers of whole genomes with known sequence characteristics based on direct sampling of experimentally known or theorized variations. | standalone software, unix/linux, mac os x, windows, java, mapreduce |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24885193 | Free, Public | OMICS_04164 | SCR_012064 | Frequency-based Insilico Genome Generator | 2026-08-08 11:59:39 | 3 | |||||||
|
DIYA Resource Report Resource Website 10+ mentions |
DIYA (RRID:SCR_012066) | software resource | A modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences. | standalone software, c++, java, perl, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19254921 | GNU General Public License | OMICS_04221 | SCR_012066 | Do-It-Yourself Annotator | 2026-08-08 12:00:06 | 10 | |||||||
|
Fastphylo Resource Report Resource Website 1+ mentions |
Fastphylo (RRID:SCR_012068) | software resource | A software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix. | applet |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24255987 | OMICS_04248 | SCR_012068 | 2026-08-08 11:59:57 | 2 | |||||||||
|
MrBayes Resource Report Resource Website 10000+ mentions |
MrBayes (RRID:SCR_012067) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. | applet, mac os x, unix/linux, windows |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:22357727 DOI:10.1093/sysbio/sys029 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04237 | https://sources.debian.org/src/mrbayes/ | SCR_012067 | 2026-08-08 11:59:39 | 10714 | |||||||
|
MMAX2 Resource Report Resource Website 1+ mentions |
MMAX2 (RRID:SCR_012100) | software resource | A GUI-based text annotation tool for creating and visualizing annotations. | applet, java |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05235 | SCR_012100 | 2026-08-08 11:59:57 | 1 | ||||||||||
|
iPapers Resource Report Resource Website |
iPapers (RRID:SCR_012103) | software resource | Software application that manages many PDF files of articles, whose information can be obtained by PubMed. | standalone software, mac os x |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05280 | SCR_012103 | 2026-08-08 11:59:57 | 0 | ||||||||||
|
PhyloTreePruner Resource Report Resource Website 10+ mentions |
PhyloTreePruner (RRID:SCR_012069) | software resource | A utility that uses a phylogenetic approach to refine orthology inferences made by graph-based (or other) methods. | applet |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24250218 | OMICS_04250 | SCR_012069 | 2026-08-08 12:00:06 | 34 | |||||||||
|
Connecting Overlapped Pair-End reads Resource Report Resource Website 1+ mentions |
Connecting Overlapped Pair-End reads (RRID:SCR_012102) | COPE | software resource | An efficient software tool to connect overlapping pair-end reads using k-mer frequencies. | standalone software, c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23044551 | GNU General Public License, v3 | OMICS_05256 | ftp://ftp.genomics.org.cn/pub/cope | SCR_012102 | Connecting Overlapped Pair-End | 2026-08-08 11:59:40 | 3 | |||||
|
RASP Resource Report Resource Website 100+ mentions |
RASP (RRID:SCR_012062) | software resource | Software that uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24445369 | OMICS_03392 | SCR_012062 | 2026-08-08 11:59:56 | 347 | |||||||||
|
GSim Resource Report Resource Website 1+ mentions |
GSim (RRID:SCR_012061) | software resource | Free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra. | standalone software, c++ |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_03390 | SCR_012061 | 2026-08-08 11:59:39 | 7 | |||||||||
|
CCAT (Combinatorial Code Analysis Tool) Resource Report Resource Website |
CCAT (Combinatorial Code Analysis Tool) (RRID:SCR_012028) | CCAT (Combinatorial Code Analysis Tool) | software resource | A software package for predicting genome-wide co-binding between biological regulators such as Transcription factors (TFs). | windows |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
PMID:24366875 | Apache License | OMICS_02179 | SCR_012028 | 2026-08-08 11:59:56 | 0 | |||||||
|
digitagCT Resource Report Resource Website 1+ mentions |
digitagCT (RRID:SCR_012027) | digitagCT | software resource | Software that combines digital gene expression (DGE) tags, RNA-Seq, tiling array expression data and species-comparison to explore new transcriptional regions and their specific biological features, particularly tissue expression or conservation. | digital gene expression, rna-seq |
is listed by: OMICtools has parent organization: National Institute for Research in Computer Science and Control; Brittany; France |
PMID:24357408 | OMICS_02178 | SCR_012027 | 2026-08-08 11:59:38 | 1 |
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.
