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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
IQ TREE Resource Report Resource Website 100+ mentions |
IQ TREE (RRID:SCR_021163) | data analysis software, data processing software, software application, software resource | Software tool for phylogenomic inference. | phylogenomic inference, tree of life, data analysis |
is listed by: Debian is listed by: OMICtools |
Austrian Science Fund FWF ; University of Vienna |
Free, Available for download, Freely available | OMICS_11543 | https://sources.debian.org/src/iqtree/ | SCR_021163 | SciCrunch Registry | 2026-10-24 12:48:52 | 450 | |||||||
|
QIIME2 Resource Report Resource Website 1000+ mentions |
QIIME2 (RRID:SCR_021258) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool as next generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.Enables researchers to start analysis with raw DNA sequence data and finish with publication quality figures and statistical results. Used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities. | Nucleic acid sequence data, nucleic acid sequence, fungal data, viral data, bacterial data, archaeal data, data analysis |
is used by: Tourmaline is used by: RiboSnake is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | https://github.com/qiime2/qiime2, https://sources.debian.org/src/q2-sample-classifier/ | SCR_021258 | SciCrunch Registry | Quantitative Insights Into Microbial Ecology 2 | 2026-10-24 12:48:53 | 1929 | ||||||||
|
balony Resource Report Resource Website 10+ mentions |
balony (RRID:SCR_010968) | balony | software resource | Image analysis and data inspection software for agar plates generated in high-throughput yeast genetics and genomics experiments. |
is listed by: OMICtools has parent organization: Google Code |
PMID:24305553 | OMICS_00839 | SCR_010968 | SciCrunch Registry | balony - Software for the analysis of high-throughput solid media-based screens | 2026-10-24 12:46:26 | 11 | ||||||||
|
OligoFaktory Resource Report Resource Website 1+ mentions |
OligoFaktory (RRID:SCR_010962) | OligoFaktory | software resource | A free software for Mac OS X which designs long oligos for DNA microarrays, primers for PCR, siRNAs, and more�� | is listed by: OMICtools | Free | OMICS_00829 | SCR_010962 | SciCrunch Registry | 2026-10-24 12:46:26 | 1 | |||||||||
|
ProbeMaker Resource Report Resource Website 10+ mentions |
ProbeMaker (RRID:SCR_010964) | ProbeMaker | software resource | A Java software aimed at providing a framework for design and analysis of sets of oligonucleotide probes for use in multiplex assays for nucleic acid analyses and other purposes. | java |
is listed by: OMICtools has parent organization: Uppsala University; Uppsala; Sweden |
PMID:16171527 | GNU General Public License, The community can contribute to this resource, MolTools library and the AppTools library are distributed under the, GNU Lesser General Public License | OMICS_00834 | SCR_010964 | SciCrunch Registry | 2026-10-24 12:46:26 | 13 | |||||||
|
PROBEmer Resource Report Resource Website |
PROBEmer (RRID:SCR_010965) | PROBEmer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 1, 2014, A web-based software tool that enables selecting optimal oligos for PCR applications and multiplex detection. | is listed by: OMICtools | PMID:12824409 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00835 | SCR_010965 | SciCrunch Registry | 2026-10-24 12:46:26 | 0 | ||||||||
|
ProDesign Resource Report Resource Website 10+ mentions |
ProDesign (RRID:SCR_010966) | ProDesign | analysis service resource, data analysis service, production service resource, service resource, software resource | Webserver that can be used to find oligonucleotide probe sets for microarray slides. The probes can be for individual sequences or for clusters of genes. This webserver accepts files up to 200 kb in size in order to minimize the running time. For larger files please download the program. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:17392329 | Licensed free of charge for academic use | OMICS_00837, biotools:prodesign | https://bio.tools/prodesign | SCR_010966 | SciCrunch Registry | 2026-10-24 12:46:26 | 19 | ||||||
|
MUSC DNA Microarray Database Resource Report Resource Website 1+ mentions |
MUSC DNA Microarray Database (RRID:SCR_010977) | microArrayDB, ��ArrayDB | data or information resource, data repository, database, service resource, storage service resource | Database that is a repository for DNA microarray data generated by MUSC investigators as well as researchers in the global research community. | gene expression, dna microarray |
is listed by: OMICtools is related to: ArrayQuest has parent organization: Medical University of South Carolina; South Carolina; USA |
University Research Resource Foundation ; NCI R24CA095841; NCRR P20RR016434 |
PMID:14668234 | Public, The community can contribute to this resource | OMICS_00868 | SCR_010977 | SciCrunch Registry | MUSC DNA Microarray Database and Project Management System, Medical University of South Carolina DNA Microarray Project Management System and the MUSC DNA Microarray Database, MUSC DNA Microarray Project Management System and MUSC DNA Microarray Database, ��ArrayDB, Medical University of South Carolina DNA Microarray Database | 2026-10-24 12:46:27 | 1 | |||||
|
TAD Resource Report Resource Website |
TAD (RRID:SCR_010978) | TAD | software resource | Software for an Active Server Page web interface to a relational SQL database that automates recording scores and linking them with clinical data for future interpretation. | tissue microarray |
is listed by: OMICtools has parent organization: University of Texas MD Anderson Cancer Center |
OMICS_00871 | SCR_010978 | SciCrunch Registry | TAD: Tissue Array Database, Tissue Array Database | 2026-10-24 12:46:27 | 0 | ||||||||
|
MICSA Resource Report Resource Website |
MICSA (RRID:SCR_010860) | MICSA | software resource | A software package for the identification of transcription factor binding sites in ChIP-Seq data, developed by Computational Systems Biology of Cancer group at the Bioinformatics Laboratory of Institut Curie (Paris). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Curie Institute; Paris; France |
biotools:micsa, OMICS_00447 | https://bio.tools/micsa | SCR_010860 | SciCrunch Registry | MICSA: Motif Identification for ChIP-Seq Analysis, Motif Identification for ChIP-Seq Analysis | 2026-10-24 12:46:24 | 0 | |||||||
|
CEAS Resource Report Resource Website 100+ mentions |
CEAS (RRID:SCR_010946) | CEAS | software resource | Integrates many useful tools to simplify ChIP-chip analysis for biologists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00802 | SCR_010946 | SciCrunch Registry | 2026-10-24 12:46:26 | 397 | |||||||||
|
NIA Array Analysis Resource Report Resource Website 50+ mentions |
NIA Array Analysis (RRID:SCR_010948) | NIA Array Analysis | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource, software resource | Data analysis server / software designed to test statistical significance of gene microarray data, visualize the results, and provide links to clone information and gene index. Several public datasets are also available. | gene expression, microarray, principal component analysis, significance analysis, gene annotation, anova, hierarchical clustering, pattern matching |
is listed by: OMICtools is listed by: SoftCite has parent organization: National Institute on Aging |
PMID:15734774 | OMICS_00774 | SCR_010948 | SciCrunch Registry | 2026-10-24 12:46:26 | 50 | ||||||||
|
EMMA2 Resource Report Resource Website 1+ mentions |
EMMA2 (RRID:SCR_010940) | EMMA2 | service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 17, 2017. A MAGE-compliant software platform for the collaborative analysis and integration of microarray data. |
is listed by: OMICtools has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:19200358 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00753 | SCR_010940 | SciCrunch Registry | EMMA 2 | 2026-10-24 12:46:26 | 6 | |||||||
|
XDrawChem Resource Report Resource Website |
XDrawChem (RRID:SCR_010941) | software resource | A drawing software application designed for drawing and analyzing chemical structures and reactions. | standalone software, c++, fortran |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_04961 | SCR_010941 | SciCrunch Registry | 2026-10-24 12:46:26 | 0 | |||||||||
|
M-CHiPS Resource Report Resource Website 1+ mentions |
M-CHiPS (RRID:SCR_010944) | M-CHiPS | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | A microarray data warehouse integrated with a software platform for microarray data analysis. It can be used as a LIMS for DNA chip experiments, also. Unlike other microarray data repositories, it entirely dispenses with free-text format, instead holding all the information in a format ready for statistical analysis. | hybridization | is listed by: OMICtools | Account required | OMICS_00771 | SCR_010944 | SciCrunch Registry | Multi-Conditional Hybridization Intensity Processing System | 2026-10-24 12:46:26 | 3 | |||||||
|
MethLAB Resource Report Resource Website 1+ mentions |
MethLAB (RRID:SCR_010957) | MethLAB | software resource | A GUI software package for analysis of DNA methylation microarray data. |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA |
OMICS_00797 | SCR_010957 | SciCrunch Registry | 2026-10-24 12:46:26 | 8 | ||||||||||
|
RnBeads Resource Report Resource Website 100+ mentions |
RnBeads (RRID:SCR_010958) | RnBeads | software resource | An R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution, including Infinium 450K microarray and bisulfite sequencing protocols, but also MeDIP-seq and MBD-seq., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00800 | SCR_010958 | SciCrunch Registry | 2026-10-24 12:46:26 | 299 | |||||||||
|
FastDMA Resource Report Resource Website 1+ mentions |
FastDMA (RRID:SCR_010954) | FastDMA | software resource | A software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which is featured as multiple core parallel computing. | is listed by: OMICtools | OMICS_00794 | SCR_010954 | SciCrunch Registry | 2026-10-24 12:46:26 | 2 | ||||||||||
|
Marmal-aid Resource Report Resource Website 10+ mentions |
Marmal-aid (RRID:SCR_010956) | Marmal-aid | data or information resource, database, software resource | A combined database and R package that allows you to investigate the methylation state of regions of interest across the genome. | is listed by: OMICtools | PMID:24330312 | Acknowledgement requested | OMICS_00796 | SCR_010956 | SciCrunch Registry | 2026-10-24 12:46:26 | 20 | ||||||||
|
CNVPartition Resource Report Resource Website 100+ mentions |
CNVPartition (RRID:SCR_010925) | CNVPartition | software resource | Software that estimates copy number and annotates regions with copy number variants(CNV). | is listed by: OMICtools | OMICS_00716 | SCR_010925 | SciCrunch Registry | 2026-10-24 12:46:26 | 135 |
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