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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Asterias Resource Report Resource Website 1+ mentions |
Asterias (RRID:SCR_010936) | Asterias | software resource | A set of web-based applications for the analysis of genomic and proteomic data. Asterias combines Python with R and C/C++, using MPI for parallelization, and aspires to become a standard for high-performance, distributed, web-based bioinformatics and biostatistics applications. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Spanish National Cancer Research Center |
PMID:17488846 | Public | OMICS_00747, biotools:asterias | https://bio.tools/asterias | SCR_010936 | 2026-08-08 11:59:39 | 1 | ||||||
|
Chipster Resource Report Resource Website 50+ mentions |
Chipster (RRID:SCR_010939) | Chipster | software resource | A user-friendly analysis software for high-throughput data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00751, biotools:chipster | https://bio.tools/chipster | SCR_010939 | 2026-08-08 11:59:39 | 85 | ||||||||
|
NucHunter Resource Report Resource Website 1+ mentions |
NucHunter (RRID:SCR_010894) | NucHunter | software resource | Software for inferring nucleosome positions with their histone mark annotation from ChIP data. It is a versatile tool that can be used to predict positioned nucleosomes from one or multiple ChIP-seq bam files and it can be also used in conjunction with a control experiment. |
is listed by: OMICtools has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
PMID:23981350 | OMICS_00509 | SCR_010894 | 2026-08-08 11:59:25 | 4 | |||||||||
|
Ginkgo Resource Report Resource Website 50+ mentions |
Ginkgo (RRID:SCR_010931) | Ginkgo | software resource | A spotted microarray data pre-processing platform featuring analysis functionalities for CGH and expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: J. Craig Venter Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00725 | SCR_010931 | Ginkgo: CGH and Expression Microarray Statistical Analysis and Normalization Platform | 2026-08-08 11:59:39 | 61 | ||||||||
|
PlnTFDB Resource Report Resource Website 100+ mentions |
PlnTFDB (RRID:SCR_010899) | data or information resource, production service resource, data analysis service, database, analysis service resource, service resource | Public database arising from efforts to identify and catalogue all plant genes involved in transcriptional control.Integrative plant transcription factor database that provides web interface to access large sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. Provides access point to its daughter databases of species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags, domain architecture and scientific literature is provided for each family. | protein model, protein sequence, gene family, protein, transcriptional control, blast, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
University of Potsdam ; Germany ; German Federal Ministry of Education and Research ; Fond der Chemischen Industrie |
PMID:19858103 PMID:17286856 |
Free, Freely available | biotools:plntfdb, OMICS_00561 | http://plntfdb.bio.uni-potsdam.de/v3.0/, https://bio.tools/plntfdb | SCR_010899 | Plant Transcription Factor Database, PlnTFDB v3.0 | 2026-08-08 11:59:39 | 218 | |||||
|
arrayMagic Resource Report Resource Website 1+ mentions |
arrayMagic (RRID:SCR_010933) | arrayMagic | software resource | Software providing a collection of utilities for quality control and processing of two-colour cDNA microarray data |
is listed by: OMICtools has parent organization: Bioconductor |
BSD License | OMICS_00743 | SCR_010933 | arrayMagic - two-colour cDNA array quality control and preprocessing | 2026-08-08 11:59:40 | 1 | ||||||||
|
Piranha Resource Report Resource Website 100+ mentions |
Piranha (RRID:SCR_010903) | Piranha | software resource | A peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00568 | SCR_010903 | Piranha -- CLIP- and RIP-Seq peak caller | 2026-08-08 11:59:39 | 173 | ||||||||
|
MethMarker Resource Report Resource Website 1+ mentions |
MethMarker (RRID:SCR_010908) | MethMarker | software resource | Tool that facilitates the design and optimization of gene-specific DNA methylation assays. Beyond its use as an epigenetic primer-design tool, it provides extensive support for epigenetic biomarker optimization. Download MethMarker or start it directly from within your web browser. | dna methylation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
PMID:19804638 | Acknowledgement requested | OMICS_00636, biotools:methmarker | https://bio.tools/methmarker | SCR_010908 | 2026-08-08 11:59:40 | 3 | ||||||
|
MOSAiCS Resource Report Resource Website 10+ mentions |
MOSAiCS (RRID:SCR_010861) | MOSAiCS | software resource | Software developed as a flexible mixture modeling approach for detecting peaks of one-sample (ChIP sample) or two-sample (ChIP sample and matched control sample) ChIP-seq data. |
is listed by: OMICtools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
OMICS_00448 | SCR_010861 | MOdel-based one and two Sample Analysis and inference for ChIP-Seq Data | 2026-08-08 11:59:38 | 28 | |||||||||
|
SISSRs Resource Report Resource Website 10+ mentions |
SISSRs (RRID:SCR_010866) | SISSRs | software resource | Anl algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments. | perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:18684996 PMID:22130889 |
biotools:sissrs, OMICS_00463 | https://bio.tools/sissrs | SCR_010866 | Site Identification from Short Sequence Reads | 2026-08-08 11:59:25 | 16 | ||||||
|
SoyDB Resource Report Resource Website 10+ mentions |
SoyDB (RRID:SCR_010900) | SoyDB | data or information resource, production service resource, data analysis service, database, analysis service resource, service resource | A Knowledge Database of Soybean Transcription Factors. PSI-BLAST is available to find hits from the database. | transcription factor, blast, amino acid sequence, predicted tertiary structure, dna binding site, domain prediction, homologous protein, protein family classification, multiple sequence alignment, dna binding motif, protein family |
is listed by: OMICtools has parent organization: University of Missouri; Missouri; USA |
NSF | PMID:20082720 | Free, Public | OMICS_00563 | SCR_010900 | SoyDB: A Knowledge Database of Soybean Transcription Factors | 2026-08-08 11:59:25 | 10 | |||||
|
ZINBA Resource Report Resource Website 10+ mentions |
ZINBA (RRID:SCR_010868) | ZINBA | software resource | Software to identify genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:21787385 | GNU General Public License, v3 | biotools:zinba, OMICS_00465 | https://bio.tools/zinba | SCR_010868 | zinba - Zero Inflated Negative Binomial Algorithm, Zero Inflated Negative Binomial Algorithm | 2026-08-08 11:59:38 | 13 | |||||
|
POLYPHEMUS Resource Report Resource Website 10+ mentions |
POLYPHEMUS (RRID:SCR_010870) | POLYPHEMUS | software resource | R package for comparative analysis of RNA Polymerase II ChIP-Seq profiles by non-linear normalization. | is listed by: OMICtools | PMID:22156059 | OMICS_00468 | SCR_010870 | 2026-08-08 11:59:39 | 12 | |||||||||
|
PPSEQ Resource Report Resource Website |
PPSEQ (RRID:SCR_010913) | PPSEQ | software resource | A software suite including a scalable hierarchical multitasking parallel infrastructure and the classical sequencing algorithms. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00677 | SCR_010913 | PPSEQ: Parallel Processing for Next-Generation Sequencing (NGS) Analysis | 2026-08-08 11:59:39 | 0 | ||||||||
|
ADaCGH Resource Report Resource Website 1+ mentions |
ADaCGH (RRID:SCR_010916) | ADaCGH | production service resource, software resource, data analysis service, analysis service resource, service resource | A web tool for the analysis of aCGH data sets. They focus on calling gains and losses and estimating the number of copy changes. Note: ADaCGH will continue being maintained, but is deprecated. Their new tool for CGH and CNV is WaviCGH, http://wavi.bioinfo.cnio.es/ | is listed by: OMICtools | PMID:17710137 | Acknowledgement requested, Free | OMICS_00700 | SCR_010916 | Analysis of data from aCGH, ADaCGH: analysis of data from aCGH | 2026-08-08 11:59:39 | 1 | |||||||
|
Agilent CytoGenomics software Resource Report Resource Website 100+ mentions |
Agilent CytoGenomics software (RRID:SCR_010917) | Agilent CytoGenomics software | software resource | Software for a complete CGH and CGH+SNP microarray data analysis and data reporting solution to streamline the day-to-day cytogenetic sample analysis research workflow. | is listed by: OMICtools | OMICS_00701 | SCR_010917 | 2026-08-08 11:59:25 | 122 | ||||||||||
|
Aroma.affymetrix Resource Report Resource Website 10+ mentions |
Aroma.affymetrix (RRID:SCR_010919) | Aroma.affymetrix | software resource | An R package for analyzing large Affymetrix data sets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00703, biotools:aroma.affymetrix | https://bio.tools/aroma.affymetrix | SCR_010919 | 2026-08-08 11:59:39 | 34 | ||||||||
|
diffReps Resource Report Resource Website 100+ mentions |
diffReps (RRID:SCR_010873) | diffReps | software resource | Finding differential chromatin modification sites from ChIP-seq data. | is listed by: OMICtools | OMICS_00472 | SCR_010873 | 2026-08-08 11:59:39 | 156 | ||||||||||
|
AlignACE Resource Report Resource Website 1+ mentions |
AlignACE (RRID:SCR_010875) | AlignACE | software resource | A software program which finds sequence elements conserved in a set of DNA sequences. | is listed by: OMICtools | PMID:10698627 | OMICS_00475 | SCR_010875 | 2026-08-08 11:59:25 | 5 | |||||||||
|
Arpeggio Resource Report Resource Website 50+ mentions |
Arpeggio (RRID:SCR_010876) | Arpeggio | software resource | Software for harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23873955 | OMICS_00476 | SCR_010876 | Arpeggio - Harmonic analysis of ChIP-seq experiments | 2026-08-08 11:59:39 | 83 |
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.
