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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ProDesign Resource Report Resource Website 10+ mentions |
ProDesign (RRID:SCR_010966) | ProDesign | production service resource, software resource, data analysis service, analysis service resource, service 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 | 2026-08-08 11:59:40 | 19 | ||||||
|
PMTED Resource Report Resource Website 1+ mentions |
PMTED (RRID:SCR_010854) | PMTED | data or information resource, production service resource, data analysis service, database, analysis service resource, service resource | A Plant MicroRNA Target Expression Database to study the microRNA (miRNA) functions by inferring their target gene expression profiles among the large amount of existing microarray data. You may also predict your miRNA targets and retrieve their microarray expression data. | gene expression, target, bioprocess, microrna, condition | is listed by: OMICtools | National High-tech Development Plan 863 Program | OMICS_00413 | SCR_010854 | Plant MicroRNA Target Expression Database | 2026-08-08 11:59:38 | 6 | |||||||
|
dPeak Resource Report Resource Website 1+ mentions |
dPeak (RRID:SCR_010855) | dPeak | software resource | A high resolution transcription factor binding site (TFBS) identification (deconvolution) algorithm. dPeak implements a probabilistic model that accurately describes ChIP-exo and ChIP-Seq data generation process for both the SET and PET assays. | chip-seq |
is listed by: OMICtools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:24146601 | OMICS_00437 | SCR_010855 | dPeak: High Resolution TFBS Identification using ChIP-exo PET and SET ChIP-Seq Data | 2026-08-08 11:59:38 | 4 | |||||||
|
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 | MICSA: Motif Identification for ChIP-Seq Analysis, Motif Identification for ChIP-Seq Analysis | 2026-08-08 11:59:25 | 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 | 2026-08-08 11:59:40 | 397 | |||||||||
|
NIA Array Analysis Resource Report Resource Website 50+ mentions |
NIA Array Analysis (RRID:SCR_010948) | NIA Array Analysis | data or information resource, production service resource, software resource, data analysis service, data set, analysis service resource, service 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 | 2026-08-08 11:59:41 | 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 | EMMA 2 | 2026-08-08 11:59:25 | 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 | 2026-08-08 11:59:41 | 0 | |||||||||
|
M-CHiPS Resource Report Resource Website 1+ mentions |
M-CHiPS (RRID:SCR_010944) | M-CHiPS | data or information resource, production service resource, data analysis service, database, analysis service resource, service resource, storage service resource, data repository | 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 | Multi-Conditional Hybridization Intensity Processing System | 2026-08-08 11:59:25 | 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 | 2026-08-08 11:59:26 | 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 | 2026-08-08 11:59:41 | 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 | 2026-08-08 11:59:26 | 2 | ||||||||||
|
Marmal-aid Resource Report Resource Website 10+ mentions |
Marmal-aid (RRID:SCR_010956) | Marmal-aid | database, data or information resource, 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 | 2026-08-08 11:59:40 | 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 | 2026-08-08 11:59:40 | 135 | ||||||||||
|
GenoSNP Resource Report Resource Website 1+ mentions |
GenoSNP (RRID:SCR_010928) | GenoSNP | software resource | A genotyping algorithm for the Illumina Infinium SNP genotyping assay. | is listed by: OMICtools | OMICS_00722 | SCR_010928 | 2026-08-08 11:59:25 | 5 | ||||||||||
|
LASAGNA-Search Resource Report Resource Website 10+ mentions |
LASAGNA-Search (RRID:SCR_010883) | LASAGNA-Search | database, data or information resource, software resource | An integrated web tool for transcription factor binding site search and visualization. Both the Python Scripts for Offline Scanning and the Python implementation of the LASAGNA algorithm are available., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor binding site |
is listed by: OMICtools has parent organization: University of Connecticut; Connecticut; USA |
PMID:23599922 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00485 | SCR_010883 | LASAGNA-Search 2.0: Searching for transcription factor binding sites (TFBSs), LASAGNA-Search: Searching for transcription factor binding sites, Length-Aware Site Alignment Guided by Nucleotide Association Search | 2026-08-08 11:59:39 | 39 | ||||||
|
RSAT peak-motifs Resource Report Resource Website 100+ mentions |
RSAT peak-motifs (RRID:SCR_010886) | Peak-motifs | software resource | Software tool that predicts motifs in full-size peak sets. It performs all steps from motif discovery to visualization of the predicted sites in genome browsers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: Free University of Brussels; Brussels; Belgium |
PMID:22156162 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00492 | SCR_010886 | 2026-08-08 11:59:25 | 226 | ||||||||
|
TFFM Resource Report Resource Website 1+ mentions |
TFFM (RRID:SCR_010888) | TFFM | software resource | Software for Transcription Factor Flexible Models (TFFMs) that represent Transcription Factor Binding Sites (TFBSs) and are based on hidden Markov models (HMM). They are flexible and are able to model both position interdependence within TFBSs and variable length motifs within a single dedicated framework. | python | is listed by: OMICtools | PMID:24039567 | GNU Lesser General Public Licence | OMICS_00495 | SCR_010888 | Transcription Factor Flexible Models | 2026-08-08 11:59:38 | 1 | ||||||
|
NOrMAL Resource Report Resource Website 50+ mentions |
NOrMAL (RRID:SCR_010889) | NOrMAL | software resource | A command line software tool for accurate placing of the nucleosomes using a Modified Gaussian Mixture Model. It was designed to resolve overlapping nucleosomes and extract extra information (fuzziness, probability, etc.) of nucleosome placement. To achieve this goal the tool clusters the input tags according to Nucleosome Model (see the paper for detailed description) using EM learning process. The tool is written in C++. There are no special requirements except for g++ compiler and *nix environment to compile and use the tool. It was checked to compile using g++ compiler under Ubuntu 11.04 and Mac OS X 10.6 | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Riverside; California; USA |
Free for academic use | OMICS_00504, biotools:normal | https://bio.tools/normal | SCR_010889 | NOrMAL: Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model | 2026-08-08 11:59:25 | 84 | ||||||
|
NucDe Resource Report Resource Website |
NucDe (RRID:SCR_010893) | NucDe | software resource | An R package mapping nucleosome-linker boundaries from both MNase-Chip and MNase-Seq data using a non-homogeneous hidden-state model based on first order differences of experimental data along genomic coordinates. |
is listed by: OMICtools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
OMICS_00508 | SCR_010893 | 2026-08-08 11:59:38 | 0 |
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