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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Monoclonal Antibody Index Resource Report Resource Website |
Monoclonal Antibody Index (RRID:SCR_013227) | MAI | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 13, 2016. A searchable biotechnology database e-books with information on more than 9000 monoclonal antibodies. This database has antibodies produced for the diagnosis and therapy of human cancer, Alzheimer's disease, AIDS, and other diseases as well as for biomarker and proteomics research. Information such as antibody name, species, type, characteristics, antigen characteristics, and developer or distributor of antibody as well as mentions in journals, patents, abstracts and reports up until 2012 are included. | antibody, monoclonal antibody, cancer, aids, sars, heart disease, vascular disease, coagulation disease, transplantation, inflammation, alzheimer's disease, autoimmunity, biomarker, proteomics, resource, research, database | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01773 | SCR_013227 | 2026-09-12 01:02:10 | 0 | ||||||||
|
DSAP Resource Report Resource Website 1+ mentions |
DSAP (RRID:SCR_013352) | DSAP | analysis service resource, data analysis service, production service resource, service resource | A web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20478825 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:dsap, OMICS_00357 | https://bio.tools/dsap | SCR_013352 | 2026-09-12 01:02:11 | 8 | ||||||
|
Drosophila melanogaster Exon Database Resource Report Resource Website 1+ mentions |
Drosophila melanogaster Exon Database (RRID:SCR_013441) | DEDB | data or information resource, database | Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers. | exon, gene, alternative splicing, annotation, classification, cluster, domain, genome, graph, homology, protein, splicing, structure, transcript, visualize, blast |
is listed by: OMICtools is related to: FlyBase has parent organization: National University of Singapore; Singapore; Singapore |
Agency for Science Technology and Research | PMID:15581431 | nif-0000-21118, OMICS_01894 | SCR_013441 | DEDB - Drosophila melanogaster Exon Database, DEDB : Drosophila melanogaster Exon Database | 2026-09-12 01:02:11 | 2 | ||||||
|
RARTF Resource Report Resource Website 1+ mentions |
RARTF (RRID:SCR_013457) | RARTF | data or information resource, database | Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available. | transcription factor, protein, gene, microarray, expression profile |
is listed by: OMICtools is related to: InterProScan |
PMID:16769687 | Free | OMICS_00562 | SCR_013457 | RARTF: RIKEN Arabidopsis Transcription Factor database, RIKEN Arabidopsis Transcription Factor database | 2026-09-12 01:02:12 | 2 | ||||||
|
cwltool Resource Report Resource Website 10+ mentions |
cwltool (RRID:SCR_015528) | software resource, software toolkit, source code | Reference implementation of the Common Workflow Language standards. It provides complete features and tools and comprehensive validation of CWL. The reference implementation consists of two packages. The cwltool package is the primary Python module containing the reference implementation in the cwltool module and console executable by the same name. The cwlref-runner package is optional and provides an additional entry point under the alias cwl-runner, which is the implementation-agnostic name for the default CWL interpreter installed on a host. | language, reference implementation, python |
uses: Python Programming Language is listed by: Debian is listed by: OMICtools |
DOI:10.6084/m9.figshare.3115156.v2 | Available for download | OMICS_28977 | https://sources.debian.org/src/cwltool/ | SCR_015528 | CWLtool, Common Workflow Language Tool | 2026-09-12 01:02:15 | 25 | ||||||
|
miRWalk Resource Report Resource Website 1000+ mentions |
miRWalk (RRID:SCR_016509) | data or information resource, database | Software tool to store the predicted and the experimentally validated microRNA (miRNA)-target interaction pairs. Predictions within the complete sequence of genes of human, mouse, and rat genomes. Integrates a comparative platform of miRNA-binding sites resulting from ten different prediction datasets. | microRNA, target, interaction, pair, binding, site, sequence, gene, data, FASEB list | is listed by: OMICtools | PMID:26226356 | Free, Available for download, Freely available | SCR_016509 | 2026-09-12 01:02:17 | 1741 | |||||||||
|
CLC Main Workbench Resource Report Resource Website 10+ mentions |
CLC Main Workbench (RRID:SCR_000354) | CLC Main Workbench | software resource, software toolkit | A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management. | sequencing, analysis, cloning, data, management, molecular, gene, genome, dna, rna |
is listed by: OMICtools is listed by: SoftCite |
Restricted | OMICS_01813 | SCR_000354 | 2026-09-12 01:02:23 | 31 | ||||||||
|
4Peaks Resource Report Resource Website 10+ mentions |
4Peaks (RRID:SCR_000015) | 4Peaks | software application, software resource | Software application for viewing and editing sequence trace files. | mac os x, sequence, trace file | is listed by: OMICtools | Free | OMICS_01015 | SCR_000015 | 2026-09-12 01:02:22 | 15 | ||||||||
|
MetAssign Resource Report Resource Website 1+ mentions |
MetAssign (RRID:SCR_000092) | software application, software resource, standalone software | Software that combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download. | peak annotation, peaks probabilistic identifications, |
is listed by: OMICtools is listed by: SourceForge has parent organization: University of Glasgow; Glasgow; United Kingdom |
PMID:24916385 | Free, Available for download, Freely available | OMICS_04679 | http://mzmatch.sourceforge.net/ | SCR_000092 | 2026-09-12 01:02:22 | 1 | |||||||
|
metaMA Resource Report Resource Website |
metaMA (RRID:SCR_000408) | software resource, software toolkit | Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools is listed by: CRAN is related to: SMAGEXP |
Scottish Government Rural and Environment Research and Analysis Directorate | PMID:19628502 | Free, Available for download, Freely available | OMICS_03524 | SCR_000408 | Meta-analysis for MicroArrays, Meta analysis for MicroArrays | 2026-09-12 01:02:23 | 0 | ||||||
|
Annotare Resource Report Resource Website |
Annotare (RRID:SCR_000319) | software application, software resource, standalone software | A software tool for annotating biomedical investigations and the resulting data, then producing a MAGE-TAB file. This software is a standalone desktop which features: an editor function, an annotation modifier, incorporation of terms from biomedical ontologies, standard templates for common experiment types, a design aid to help create a new document, and a validator that checks for syntactic and semantic violations. | biomedical research, magetab, editor, annotation, biomedical ontology | is listed by: OMICtools | NIBIB ; NCI ; NHGRI P41 HG003619 |
PMID:20733062 | Free, Available for download, Freely available | OMICS_00741 | SCR_000319 | annotare: a tool for annotating high-throughput biomedical investigations and resulting data | 2026-09-12 01:02:23 | 0 | ||||||
|
PEPPER Resource Report Resource Website 1+ mentions |
PEPPER (RRID:SCR_000431) | PEPPER | software application, software resource | A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...). | plugin, protein-protein interaction, network, bio.tools |
is listed by: OMICtools is listed by: Cytoscape is listed by: bio.tools is listed by: Debian |
PMID:25138169 | Free, Available for download, Freely available | biotools:pepper, OMICS_05485 | https://bio.tools/pepper | SCR_000431 | Protein complex Expansion using Protein-Protein intERaction networks, Protein complex Expansion using Protein-Protein intERactions | 2026-09-12 01:02:23 | 1 | |||||
|
ADEGENET Resource Report Resource Website 10+ mentions Issue |
ADEGENET (RRID:SCR_000825) | ADEGENET | software application, software resource | Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic, r |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
PMID:21926124 PMID:18397895 DOI:10.1093/bioinformatics/btn129 |
Free, Available for download, Freely available | nlx_153996, nlx_154580, OMICS_11078, SCR_007239 | http://adegenet.r-forge.r-project.org/, https://sources.debian.org/src/r-cran-adegenet/ | SCR_000825 | R/ADEGENET | 2026-09-12 01:02:24 | 22 | |||||
|
Illuminate Resource Report Resource Website 1+ mentions |
Illuminate (RRID:SCR_000178) | Illuminate | software resource, software toolkit | Python module and utilities to parse the metrics binaries output by Illumina sequencers, and provides usable data in the form of python dictionaries and dataframes. Intended to emulate the output of Illumina SAV, it allows you to print sequencing run metrics to the command line as well as work with the data programmatically. | illumina, python | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02102 | SCR_000178 | Illuminate - Analytics toolkit for Illumina sequencer metrics | 2026-09-12 01:02:23 | 1 | |||||||
|
NGS-Cleaner Resource Report Resource Website |
NGS-Cleaner (RRID:SCR_000574) | NGS-Cleaner | software application, software resource | Software application that provides cleaning of FASTQ/A formatted large DNA sequence files containing multiple short-reads sequences provided by Next Generation Sequencing platforms. | next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available, | OMICS_01166 | SCR_000574 | 2026-09-12 01:02:23 | 0 | ||||||||
|
Chromas Resource Report Resource Website 10+ mentions |
Chromas (RRID:SCR_000598) | Chromas | commercial organization, software resource | Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01016, biotools:chromas | https://bio.tools/chromas | SCR_000598 | 2026-09-12 01:03:10 | 16 | |||||||
|
GenVision Resource Report Resource Website 1+ mentions |
GenVision (RRID:SCR_001166) | GenVision | commercial organization, software resource | A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig. | genome, image, visualization, graphic, map, gene expression, contig, genetics |
is listed by: OMICtools works with: Lasergene's SeqMan Pro |
Commercial | OMICS_02135 | SCR_001166 | GenVision - Software for Publication-Quality Illustrations, DNASTAR GenVision | 2026-09-12 01:03:11 | 1 | |||||||
|
Sequence Search and Alignment by Hashing Algorithm Resource Report Resource Website 1+ mentions |
Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) | SSAHA2 | software resource, source code | A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported. | sequence, genomic, analysis, search, alignment, algorithm, mapping, bio.tools |
is listed by: OMICtools is listed by: bio.tools is related to: SMALT has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:11591649 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ssaha2, OMICS_00690, nlx_93831 | https://bio.tools/ssaha2 | SCR_000544 | ssaha2, ssaha, Sequence Search and Alignment by Hashing Algorithm | 2026-09-12 01:03:09 | 6 | |||||
|
DecGPU Resource Report Resource Website 1+ mentions |
DecGPU (RRID:SCR_000585) | software resource | Software tool as parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models. | k-mer based corrector, k-mer spectrum, illumina short read, multistage workflow, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21447171 | Free, Available for download, Freely available | biotools:decgpu, OMICS_01101, SCR_011850, OMICS_01060 | http://musket.sourceforge.net/homepage.htm#latest, https://bio.tools/decgpu | SCR_000585 | Distributed short read Error Correction on GPUs | 2026-09-12 01:03:10 | 5 | ||||||
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CodonCodes TraceViewer Resource Report Resource Website 1+ mentions |
CodonCodes TraceViewer (RRID:SCR_002304) | TraceViewer | commercial organization, software resource | A Java program that allows you to see, print, and edit DNA sequencing traces. | windows, dna sequencing trace, dna, sequencing, trace | is listed by: OMICtools | Free for academic use | OMICS_01822 | SCR_002304 | CodonCode''s TraceViewer | 2026-09-12 01:03:12 | 1 |
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