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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NTAP Resource Report Resource Website 10+ mentions |
NTAP (RRID:SCR_001488) | NTAP | data analysis software, software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for tiling array data analysis to survey the genome-wide binding sites of transcription factor HY5 in Arabidopsis and the genome-wide histone modifications/DNA methylation level in rice. It was developed in the process of generating NimbleGen analysis. Written in R and Perl. | software, tiling array, data analysis, rice, arabidopsis, hy5, transcription factor, genome |
is listed by: OMICtools has parent organization: Peking University; Beijing; China |
PMID:19468055 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00808 | SCR_001488 | NimbleGen Tiling array Analysis Package, NimbleGen Tilingarray Analysis Package | 2026-08-06 09:25:23 | 10 | ||||||
|
FusionCatcher Resource Report Resource Website 1+ mentions |
FusionCatcher (RRID:SCR_000060) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software that searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. | fusion gene, known fusion gene, translocation, chimera, rna-seq data, hiseq, solexa, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/011650 | Free, Available for download, Freely available | biotools:fusioncatcher, OMICS_01348 | https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md, https://bio.tools/fusioncatcher | http://code.google.com/p/fusioncatcher/ | SCR_000060 | 2026-08-06 09:25:06 | 7 | ||||||
|
Dissect Resource Report Resource Website |
Dissect (RRID:SCR_000058) | Dissect | software resource, alignment software, image analysis software, data processing software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. | Structural events containing transcripts, transcriptome-to-genome alignment, identify and characterize transcriptomic events, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Simon Fraser University; British Columbia; Canada |
PMID:22689759 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01346, biotools:dissect | https://bio.tools/dissect | SCR_000058 | Dissect: DIScovery of Structural Events Containing Transcripts, DIScovery of Structural Events Containing Transcripts | 2026-08-06 09:25:06 | 0 | |||||
|
GeneMark Resource Report Resource Website 500+ mentions |
GeneMark (RRID:SCR_011930) | GeneMark | software resource, service resource, production service resource, data analysis service, analysis service resource | A family of gene prediction programs developed at Georgia Institute of Technology. |
is listed by: OMICtools has parent organization: Georgia Institute of Technology; Georgia; USA |
Academic License Agreement | OMICS_01485 | SCR_011930 | 2026-08-06 09:27:50 | 768 | |||||||||
|
Annmap Resource Report Resource Website 1+ mentions |
Annmap (RRID:SCR_011783) | Annmap | database, data or information resource, software resource | A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser. | is listed by: OMICtools | Cancer Research UK ; Cancer Research UK Manchester Institute |
OMICS_00900 | SCR_011783 | 2026-08-06 09:27:50 | 6 | |||||||||
|
UNC Microarray Database Resource Report Resource Website 10+ mentions |
UNC Microarray Database (RRID:SCR_010979) | UNC MD, UNCMD | storage service resource, service resource, data repository, data or information resource, database | Database for microarray data storage, retrieval, analysis, and visualization. | microarray, FASEB list |
is listed by: OMICtools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Account required, The community can contribute to this resource | OMICS_00872 | SCR_010979 | UNC-Chapel Hill Microarray Database | 2026-08-06 09:27:41 | 31 | |||||||
|
B-Fabric Resource Report Resource Website 1+ mentions |
B-Fabric (RRID:SCR_011827) | B-Fabric | storage service resource, service resource, data repository, data or information resource, database | An open infrastructure for managing projects and data in life sciences that allows to store and access experimental data together with its scientific context. The platform connects the data from scientific instruments with data analysis tools, including workflow, annotation, and data visualization support. All public data can be searched and used to carry out inter-experiment analyses. For a fee, B-Fabric Order allows you to order the following analytical services at the FGCZ independent of a User Lab research project: Mass spectrometry, Protein sequencing, peptide sequencing, Amino acid analysis, Chromatography, Electrophoresis. | project management, mass spectrometry, protein sequencing, peptide sequencing, amino acid analysis, chromatography, electrophoresis |
is listed by: OMICtools has parent organization: University of Zurich; Zurich; Switzerland |
PMID:21772064 | Account required | OMICS_01002 | SCR_011827 | 2026-08-06 09:27:50 | 1 | |||||||
|
miRTar Resource Report Resource Website 50+ mentions |
miRTar (RRID:SCR_010851) | miRTar | data set, service resource, production service resource, data analysis service, data or information resource, analysis service resource | An integrated web server for identifying miRNA-target interactions in human. The tool enables biologists easily to identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts. |
is listed by: OMICtools has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
OMICS_00410 | SCR_010851 | MicroRNA Target prediction | 2026-08-06 09:27:41 | 52 | |||||||||
|
TBLASTX Resource Report Resource Website 1000+ mentions |
TBLASTX (RRID:SCR_011823) | TBLASTX | web application, software resource | A web-based tool used to search translated nucleotide databases using a translated nucleotide query. | nucleotide database, web based, nucleotide query |
is listed by: OMICtools has parent organization: NCBI |
Available to the research community | OMICS_01000 | SCR_011823 | Translated BLAST: tblastx | 2026-08-06 09:27:49 | 1446 | |||||||
|
MetAMOS Resource Report Resource Website 10+ mentions |
MetAMOS (RRID:SCR_011914) | MetAMOS | software application, workflow software, data processing software, software resource | A modular and open source metagenomic assembly and analysis pipeline. | microbiome, pipeline, microbiome, workflow software, metagenomic assembly, metagenomic assembly, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: bio.tools is listed by: Debian is hosted by: GitHub |
Open source, Available for download | OMICS_01426, biotools:metamos | https://github.com/marbl/metAMOS, https://bio.tools/metamos | SCR_011914 | 2026-08-06 09:27:50 | 14 | |||||||
|
Antibody Portal Resource Report Resource Website |
Antibody Portal (RRID:SCR_011995) | Antibody Portal | commercial organization, material resource, reagent supplier, antibody supplier | Serves as a gateway that provides visible access to a large number of reagents and accompanying characterization data to the research and industrial community. | is listed by: OMICtools | OMICS_01767 | SCR_011995 | 2026-08-06 09:27:50 | 0 | ||||||||||
|
Antibody Validation Database Resource Report Resource Website 10+ mentions |
Antibody Validation Database (RRID:SCR_011996) | Antibody Validation Database | storage service resource, service resource, data repository, data or information resource, database | The aim of this site is to collect and to share experimental results on antibodies that would otherwise remain in laboratories, thus aiding researchers in selection and validation of antibodies. | is listed by: OMICtools | OER U01 ES017166; NHGRI U01 HG004258; NHGRI U01 HG004270 |
The community can contribute to this resource | OMICS_01769 | SCR_011996 | 2026-08-06 09:27:49 | 14 | ||||||||
|
LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data analysis software, software application, software resource, data processing software | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool, https://bio.tools/limma, https://sources.debian.org/src/r-bioc-limma/ | SCR_010943 | Linear Models for Microarray Data | 2026-08-06 09:27:41 | 24583 | ||||||
|
KisSplice Resource Report Resource Website 10+ mentions |
KisSplice (RRID:SCR_011893) | KisSplice | data analysis software, software application, software resource, data processing software | Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events. | RNA-seq data analysis, with reference genome, without reference genome, local transcriptome assembler, SNPs, indels, AS events., bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1471-2105-13-S6-S5 | Free, Available for download, Freely available | biotools:KisSplice, OMICS_01321 | https://bio.tools/KisSplice, https://sources.debian.org/src/kissplice/ | SCR_011893 | 2026-08-06 09:27:48 | 20 | ||||||
|
FISH Oracle Resource Report Resource Website |
FISH Oracle (RRID:SCR_010927) | FISH Oracle | database, data or information resource, software resource | A web-based software tool for the integrative analysis of cancer genomics data. It stores different kinds of downstream processed data from multiple samples in a single database. A powerful search interface allows to dynamically filter the data to be displayed with respect to different criteria. The combination of AJAX technology and a fast visualization engine facilitates a highly dynamic visualization for large amounts of data. FISH Oracle 2 is able to simultaneously display different data sets, thus simplifying their comparison. Filter and display options can be changed on the fly. High quality image export enables the life scientist to easily communicate the results, e.g. in presentations or publications. A comprehensive data administration assures to keep track of the data stored in the database. | array cgh, snp, genomics, visualization |
is listed by: OMICtools has parent organization: University of Hamburg; Hamburg; Germany |
Cancer | PMID:21884636 | OMICS_00721 | SCR_010927 | 2026-08-06 09:27:40 | 0 | |||||||
|
ECHO Resource Report Resource Website 100+ mentions |
ECHO (RRID:SCR_011851) | ECHO | sequence analysis software, software resource, algorithm resource, data analysis software, data processing software, software application | Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II. | error correction, rnaseq, rna sequence, short-read, next-generation sequencing, ngs, illumina, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21482625 DOI:10.1101/gr.111351.110 |
Free, Available for download | biotools:echo, OMICS_01102 | https://bio.tools/echo, https://sources.debian.org/src/uc-echo/ | SCR_011851 | ECHO: A reference-free short-read error correction algorithm | 2026-08-06 09:27:50 | 310 | |||||
|
oPOSSUM Resource Report Resource Website 100+ mentions |
oPOSSUM (RRID:SCR_010884) | oPOSSUM | software resource, service resource, production service resource, data analysis service, analysis service resource | A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences. | transcription factor binding site | is listed by: OMICtools | PMID:22973536 PMID:17576675 PMID:15933209 |
Acknowledgement requested | OMICS_00488 | SCR_010884 | oPOSSUM-3 | 2026-08-06 09:27:40 | 101 | ||||||
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CaMPDB Resource Report Resource Website 1+ mentions |
CaMPDB (RRID:SCR_011976) | CaMPDB | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | Calpain cleavage prediction using multiple kernel learning. | is listed by: OMICtools | PMID:21559271 | OMICS_01669 | SCR_011976 | Calpain for Modulatory Proteolysis Database | 2026-08-06 09:27:49 | 7 | ||||||||
|
Algal Functional Annotation Tool Resource Report Resource Website |
Algal Functional Annotation Tool (RRID:SCR_012034) | Algal Functional Annotation Tool | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest. | gene, pathway, visualization, annotation, function, protein family, ontology, protein, genomics |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: MetaCyc is related to: Reactome is related to: Pfam is related to: InterPro has parent organization: University of California at Los Angeles; California; USA |
DOE ; NAABB ; IGP ; Air Force Office of Scientific Research |
PMID:21749710 | OMICS_02226 | SCR_012034 | 2026-08-06 09:27:50 | 0 | |||||||
|
NGS Leaders Resource Report Resource Website |
NGS Leaders (RRID:SCR_011982) | NGS Leaders | portal, community building portal, data or information resource | A community created to advance the use and value of next-generation sequencing through knowledge sharing. | is listed by: OMICtools | OMICS_01707 | SCR_011982 | 2026-08-06 09:27:51 | 0 |
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