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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | SciCrunch Registry | 2026-10-17 01:27:47 | 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 | SciCrunch Registry | Transcription Factor Flexible Models | 2026-10-17 01:28:10 | 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 | SciCrunch Registry | NOrMAL: Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model | 2026-10-17 01:27:37 | 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 | SciCrunch Registry | 2026-10-17 01:27:26 | 0 | ||||||||||
|
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 | SciCrunch Registry | 2026-10-17 01:28:12 | 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 | SciCrunch Registry | 2026-10-17 01:27:27 | 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 | SciCrunch Registry | 2026-10-17 01:28:10 | 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 | SciCrunch Registry | Ginkgo: CGH and Expression Microarray Statistical Analysis and Normalization Platform | 2026-10-17 01:27:38 | 61 | ||||||||
|
PlnTFDB Resource Report Resource Website 100+ mentions |
PlnTFDB (RRID:SCR_010899) | analysis service resource, data analysis service, data or information resource, database, production 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 |
Fond der Chemischen Industrie ; German Federal Ministry of Education and Research ; University of Potsdam ; Germany |
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 | SciCrunch Registry | Plant Transcription Factor Database, PlnTFDB v3.0 | 2026-10-17 01:27:47 | 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 | SciCrunch Registry | arrayMagic - two-colour cDNA array quality control and preprocessing | 2026-10-17 01:27:27 | 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 | SciCrunch Registry | Piranha -- CLIP- and RIP-Seq peak caller | 2026-10-17 01:27:37 | 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 | SciCrunch Registry | 2026-10-17 01:27:48 | 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 | 2026-10-17 01:27:25 | 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 | 2026-10-17 01:28:09 | 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 | 2026-10-17 01:27:26 | 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 | 2026-10-17 01:27:46 | 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 | 2026-10-17 01:28:09 | 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 | 2026-10-17 01:27:48 | 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 | 2026-10-17 01:27:38 | 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 | 2026-10-17 01:27:48 | 122 |
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