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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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | SciCrunch Registry | 2026-10-24 12:46:25 | 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 | SciCrunch Registry | MOdel-based one and two Sample Analysis and inference for ChIP-Seq Data | 2026-10-24 12:46:25 | 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 | SciCrunch Registry | Site Identification from Short Sequence Reads | 2026-10-24 12:46:25 | 16 | ||||||
|
SoyDB Resource Report Resource Website 10+ mentions |
SoyDB (RRID:SCR_010900) | SoyDB | analysis service resource, data analysis service, data or information resource, database, production 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 | SciCrunch Registry | SoyDB: A Knowledge Database of Soybean Transcription Factors | 2026-10-24 12:46:25 | 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 | SciCrunch Registry | zinba - Zero Inflated Negative Binomial Algorithm, Zero Inflated Negative Binomial Algorithm | 2026-10-24 12:46:25 | 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 | SciCrunch Registry | 2026-10-24 12:46:25 | 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 | SciCrunch Registry | PPSEQ: Parallel Processing for Next-Generation Sequencing (NGS) Analysis | 2026-10-24 12:46:25 | 0 | ||||||||
|
ADaCGH Resource Report Resource Website 1+ mentions |
ADaCGH (RRID:SCR_010916) | ADaCGH | analysis service resource, data analysis service, production service resource, service resource, software 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 | SciCrunch Registry | Analysis of data from aCGH, ADaCGH: analysis of data from aCGH | 2026-10-24 12:46:26 | 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 | SciCrunch Registry | 2026-10-24 12:46:26 | 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 | SciCrunch Registry | 2026-10-24 12:46:26 | 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 | SciCrunch Registry | 2026-10-24 12:46:25 | 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 | SciCrunch Registry | 2026-10-24 12:46:25 | 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 | SciCrunch Registry | Arpeggio - Harmonic analysis of ChIP-seq experiments | 2026-10-24 12:46:25 | 83 | ||||||||
|
diChIPMunk Resource Report Resource Website 1+ mentions |
diChIPMunk (RRID:SCR_010879) | diChIPMunk | software resource | Software for motif discovery using dinucleotide position weight matrices (PWMs). | positional weight matrix, motif |
is listed by: OMICtools has parent organization: Russian Academy of Sciences; Moscow; Russia |
Dynasty Foundation ; Russian Foundation for Basic Research ; Program Cell and Molecular Biology of the Presidium of Russian Academy of Sciences ; Russian Federation Government |
PMID:23427986 | OMICS_00481 | SCR_010879 | SciCrunch Registry | diChIPMunk - motif discovery using dinucleotide PWMs | 2026-10-24 12:46:25 | 3 | ||||||
|
kmer-SVM Resource Report Resource Website 1+ mentions |
kmer-SVM (RRID:SCR_010882) | kmer-SVM | analysis service resource, data analysis service, production service resource, service resource, software resource | A webserver built on the Galaxy framework that enables the mining of sequence data for transcription factor binding sites. This tool suite was designed to aid in analysis of next-generation sequencing (NGS) data that uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. While you may use datasets already available from Galaxy, you can upload your data using the ''Get Data'' Tool. The tool can upload data from a variety of locations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA has parent organization: Galaxy |
PMID:23771147 | Acknowledgement requested | OMICS_00484, biotools:kmer-svm | https://bio.tools/kmer-svm | SCR_010882 | SciCrunch Registry | 2026-10-24 12:46:25 | 3 | ||||||
|
NURD Resource Report Resource Website 50+ mentions |
NURD (RRID:SCR_010988) | NURD | software resource | An algorithm to inference isoform expression., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:nurd, OMICS_01283 | https://bio.tools/nurd | SCR_010988 | SciCrunch Registry | 2026-10-24 12:46:27 | 72 | |||||||
|
European Medicines Agency Resource Report Resource Website 100+ mentions |
European Medicines Agency (RRID:SCR_011215) | EMA | nonprofit organization | An agency responsible for the evaluation and supervision of medicines developed by pharmaceutical companies for use in the European Union. Its main responsibility is the protection and promotion of public and animal health through the evaluation and supervision of medicines for human and veterinary use. The Agency also plays a role in stimulating innovation and research in the pharmaceutical sector. The Agency gives scientific advice and other assistance to companies for the development of new medicines. It publishes guidelines on quality-, safety- and efficacy-testing requirements. A dedicated SME Office provides special assistance to small and medium-sized enterprises. |
is listed by: OMICtools is related to: Predictive Safety Testing Consortium is related to: GetReal is related to: PharmaCog has parent organization: European Union is parent organization of: EU Clinical Trials Register |
grid.452397.e, Wikidata: Q130146, nif-0000-30532 | https://ror.org/01z0wsw92 | SCR_011215 | SciCrunch Registry | EU Medicines Agency | 2026-10-24 12:46:30 | 388 | ||||||||
|
openBIS Resource Report Resource Website 10+ mentions |
openBIS (RRID:SCR_011815) | openBIS | software resource | Software for an open, distributed system for managing biological information that supports biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for the following technologies: * High Content Screening * Proteomics * Deep Sequencing * Metabolomics |
is listed by: OMICtools has parent organization: ETH Zurich; Zurich; Switzerland |
PMID:22151573 | OMICS_01009 | SCR_011815 | SciCrunch Registry | open Biology Information System | 2026-10-24 12:46:40 | 14 | ||||||||
|
Kalign Resource Report Resource Website 100+ mentions |
Kalign (RRID:SCR_011810) | Kalign | software resource | A fast and accurate multiple sequence alignment algorithm. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
PMID:16343337 DOI:10.1093/bioinformatics/btz795 |
Free | OMICS_00978, biotools:kalign | https://bio.tools/kalign, https://sources.debian.org/src/kalign/ | SCR_011810 | SciCrunch Registry | 2026-10-24 12:46:40 | 123 | ||||||
|
MAFFT Resource Report Resource Website 10000+ mentions |
MAFFT (RRID:SCR_011811) | MAFFT | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments. | alignment, amino acid, nucleotide, sequence, DNA, sequence alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
EMBL ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:12136088 PMID:17118958 PMID:16362903 PMID:15661851 PMID:18439255 PMID:23023983 DOI:10.1093/bib/bbn013 |
biotools:MAFFT, OMICS_00979 | https://www.ebi.ac.uk/Tools/msa/mafft/, https://www.genome.jp/tools-bin/mafft, https://myhits.isb-sib.ch/cgi-bin/mafft, https://bio.tools/MAFFT, https://sources.debian.org/src/mafft/ | SCR_011811 | SciCrunch Registry | Multiple Alignment using Fast Fourier Transform, MAFFT version 5, MAFFT version 7 | 2026-10-24 12:46:40 | 24687 |
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