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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PathXL TMA Resource Report Resource Website |
PathXL TMA (RRID:SCR_005596) | PathXL TMA | commercial organization, software resource | Tissue microarray (TMA) Software used for Biomarker Discovery that allows TMA experiments to be performed anytime, anywhere, reducing administrative costs and time. It is designed to support TMA scoring workflow and allows configuration of experiments in minutes. Access and view clinical metadata, the TMA core, scoring criteria and the TMA map all on a single interface. | tissue microarray, pathology, clinical | is listed by: OMICtools | OMICS_00817 | SCR_005596 | SciCrunch Registry | 2026-09-26 02:19:48 | 0 | |||||||||
|
DNA Chromatogram Explorer Resource Report Resource Website 1+ mentions |
DNA Chromatogram Explorer (RRID:SCR_005585) | Chromatogram Explorer | commercial organization, software resource | A Windows Explorer clone dedicated to DNA sequence analysis and manipulation. View, edit, and convert chromatograms. Trim low quality ends automatically. The Lite version of Chromatogram Explorer is freeware. | chromatogram | is listed by: OMICtools | Commercial license, Free, (Lite version) | OMICS_01018 | SCR_005585 | SciCrunch Registry | DNA Chromatogram Explorer Lite, Chromatogram Explorer Lite | 2026-09-26 02:19:48 | 1 | |||||||
|
Models of SHM Targeting and Substitution Resource Report Resource Website 1+ mentions |
Models of SHM Targeting and Substitution (RRID:SCR_005250) | S5F | data or information resource, data set | A targeting model that defines where mutations occur (by specifying the relative rates at which DNA motifs in the Ig sequence are mutated), and a nucleotide substitution model that defines the resulting mutation (by specifying the probability of each base mutating to each of the other three possibilities as a function of the surrounding bases). | somatic hypermutation, substitution, targeting, aid, b cell, affinity maturation, immunoglobulin, mutability, mutation, model, targeting model, nucleotide substitution model |
is listed by: OMICtools has parent organization: Yale School of Medicine; Connecticut; USA |
PMID:24298272 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported | OMICS_00302 | SCR_005250 | SciCrunch Registry | S5F - Models of SHM Targeting and Substitution, Models of SHM Targeting and Substitution | 2026-09-26 02:19:48 | 2 | ||||||
|
MF-GE Resource Report Resource Website |
MF-GE (RRID:SCR_003509) | MF-GE | software resource, source code | A hybrid software system for feature selection and sample classification of high-dimensional datasets. It is designed for microarray but can be applied to any other high-dimensional datasets. It uses multiple filters to produce a normalized score for each feature. The score is an indication of the usefulness of each feature. It is then translated into a frequency map with more useful features receive a higher frequency in the map. | microarray, classification, gene |
is listed by: OMICtools has parent organization: University of Sydney; Sydney; Australia |
PMID:20122224 | OMICS_02295 | SCR_003509 | SciCrunch Registry | Multiple Filters enhanced Genetic Ensemble System (MF-GE), Multiple Filters enhanced Genetic Ensemble System | 2026-09-26 02:19:46 | 0 | |||||||
|
Omicsoft Sequence Aligner Resource Report Resource Website 1+ mentions |
Omicsoft Sequence Aligner (RRID:SCR_005270) | OSA | commercial organization, software resource | A fast and accurate alignment tool for RNA-Seq data. | alignment, rna-seq | is listed by: OMICtools | Free for academic use, Commercial use requires license | OMICS_01262 | SCR_005270 | SciCrunch Registry | OSA: a super-fast and accurate alignment tool for RNA-Seq data | 2026-09-26 02:19:48 | 4 | |||||||
|
VelociMapper Resource Report Resource Website |
VelociMapper (RRID:SCR_005262) | VelociMapper???? | commercial organization, software resource | Accelerated alignment tool for mapping data from next-generation DNA sequencing systems. It runs on TimeLogic''s newest FPGA-based DeCypher J-Series Similarity Search Engine Accelerator to provide fast and reliable results that significantly outperform software-only or GPU-accelerated alternatives. | next-generation sequencing | is listed by: OMICtools | Commercial license | OMICS_00696 | SCR_005262 | SciCrunch Registry | VelociMapper - Accelerated Reference Alignment Mapping Tool | 2026-09-26 02:19:48 | 0 | |||||||
|
SpliceDB Resource Report Resource Website 1+ mentions |
SpliceDB (RRID:SCR_006262) | SpliceDB | data or information resource, data set | Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs. | gene, expressed sequence tag, splice, canonical, non-canonical, splice site, sequence, data set, splice site sequence |
is listed by: OMICtools is listed by: 3DVC is related to: GenBank has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:11125105 PMID:11058137 |
nlx_151853, OMICS_01892 | http://linux1.softberry.com/berry.phtml?topic=splicedb | http://genomic.sanger.ac.uk/spldb/SpliceDB.htm | SCR_006262 | SciCrunch Registry | SpliceDB: canonical and non-canonical splice site sequences in mammalian genes | 2026-09-26 02:19:48 | 2 | |||||
|
Genomedata Resource Report Resource Website 1+ mentions |
Genomedata (RRID:SCR_004544) | Genomedata | software resource, source code | A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems. | genome, data, format, linux, mac, functional genomics, function, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:20435580 | GNU General Public License | nlx_53677, biotools:genomedata, OMICS_02148 | https://bio.tools/genomedata | SCR_004544 | SciCrunch Registry | 2026-09-26 02:19:47 | 1 | ||||||
|
RTG Variant Resource Report Resource Website |
RTG Variant (RRID:SCR_010805) | rtgVariant | commercial organization, software resource | The product line encompasses distinct products for the specific needs of clinical research, saving time and money while allowing customers to focus on the answers they need most. | is listed by: OMICtools | Commercial license | OMICS_00292 | SCR_010805 | SciCrunch Registry | Real Time Genomics (RTG Variant) | 2026-09-26 02:20:01 | 0 | ||||||||
|
Array Designer Resource Report Resource Website 1+ mentions |
Array Designer (RRID:SCR_010960) | Array Designer | commercial organization, software resource | Oligo and cDNA Microarray Design Software that designs thousands of primers and probes for oligo and cDNA microarrays in seconds. | is listed by: OMICtools | OMICS_00825 | SCR_010960 | SciCrunch Registry | 2026-09-26 02:20:01 | 2 | ||||||||||
|
GeneSpring GX Resource Report Resource Website 1000+ mentions |
GeneSpring GX (RRID:SCR_010972) | GeneSpring GX | commercial organization, software resource | Powerful, accessible statistical tools for fast visualization and analysis of microarrays - expression arrays, miRNA, exon arrays and genomics copy number data. |
is listed by: OMICtools is listed by: SoftCite |
Commercial license | OMICS_00853 | SCR_010972 | SciCrunch Registry | 2026-09-26 02:20:01 | 1817 | |||||||||
|
miRCURY LNA microRNA Array Analysis Software Resource Report Resource Website |
miRCURY LNA microRNA Array Analysis Software (RRID:SCR_010952) | miRCURY LNA microRNA Array Analysis Software | commercial organization, software resource | Software for fast and accurate analysis of miRCURY LNA microRNA Array data. | is listed by: OMICtools | Commercial license | OMICS_00786 | SCR_010952 | SciCrunch Registry | 2026-09-26 02:20:01 | 0 | |||||||||
|
RTG Metagenomics Resource Report Resource Website |
RTG Metagenomics (RRID:SCR_011949) | rtgMetagenomics | commercial organization, software resource | Delivers comprehensive shotgun metagenomics sequence analysis for accurate species frequency composition and protein searching. | is listed by: OMICtools | Commercial license | OMICS_01522 | SCR_011949 | SciCrunch Registry | Real Time Genomics (RTG Metagenomics) | 2026-09-26 02:20:06 | 0 | ||||||||
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Genomatix Solutions Resource Report Resource Website |
Genomatix Solutions (RRID:SCR_011855) | Genomatix Solutions | commercial organization, software resource | With their unique combination of proprietary algorithms and comprehensive data background, all our solutions do more than enable you to efficiently and effectively analyze and interpret biological data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is parent organization of: Genomatix Software: Understanding Gene Regulation is parent organization of: LitInspector |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01126 | SCR_011855 | SciCrunch Registry | 2026-09-26 02:20:06 | 0 | |||||||||
|
Potassium Channel Database Resource Report Resource Website 1+ mentions |
Potassium Channel Database (RRID:SCR_011960) | KDB | data or information resource, data set | A Database of Potassium Ion Channel Homology Models & Molecular Dynamics Simulations. | potassium ion channel, homology model, crystal structure, molecular dynamics, simulation, structure, image |
is listed by: OMICtools has parent organization: University of Oxford; Oxford; United Kingdom |
BBSRC ; Wellcome Trust |
OMICS_01609 | SCR_011960 | SciCrunch Registry | Potassium Channel Database - Structures and Simulations | 2026-09-26 02:20:06 | 2 | |||||||
|
CMA Resource Report Resource Website 10+ mentions |
CMA (RRID:SCR_012779) | CMA | commercial organization, software resource | A software package to do meta-analysis which works in a spreadsheet interface and also provides forest plots, which are useful for visualizing between-study heterogeneity. | is listed by: OMICtools | Commercial license | OMICS_00233 | SCR_012779 | SciCrunch Registry | Comprehensive Meta-analysis | 2026-09-26 02:20:13 | 23 | ||||||||
|
PhyloTree.org Resource Report Resource Website 100+ mentions |
PhyloTree.org (RRID:SCR_012948) | PhyloTree.org | data or information resource, data set | A phylogenetic tree of global human mitochondrial DNA variation, based on both coding- and control-region mutations, and including haplogroup nomenclature. | is listed by: OMICtools | PMID:18853457 | Free, Acknowledgement requested | OMICS_01643 | SCR_012948 | SciCrunch Registry | PhyloTree | 2026-09-26 02:20:13 | 370 | |||||||
|
FastTree Resource Report Resource Website 5000+ mentions |
FastTree (RRID:SCR_015501) | software resource, source code | Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution. | phylogenetic tree, phylogenetic tree creation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: VeryFastTree |
PMID:19377059 DOI:10.1371/journal.pone.0009490 |
biotools:fasttree, OMICS_14703 | https://bio.tools/fasttree, https://sources.debian.org/src/fasttree/ | SCR_015501 | SciCrunch Registry | 2026-09-26 02:20:23 | 6279 | ||||||||
|
phytools Resource Report Resource Website 500+ mentions |
phytools (RRID:SCR_015502) | software resource, source code | Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species. | r package, phylogenetic comparison, phylogenetic analysis |
is listed by: Debian is listed by: OMICtools is hosted by: GitHub |
DOI:10.1111/j.2041-210X.2011.00169.x | Available for download, Acknowledgement requested | OMICS_12499 | https://github.com/liamrevell/phytools, https://sources.debian.org/src/r-cran-phytools/ | SCR_015502 | SciCrunch Registry | 2026-09-26 02:20:23 | 718 | |||||||
|
NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects Resource Report Resource Website |
NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects (RRID:SCR_003205) | NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects | data or information resource, portal, project portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2025. 2012 workshop to establish a Central Resource of Data from Genome Sequencing Projects. The workshop addressed the challenges to aggregating and analyzing data sets from genome sequencing studies, such as: * Data sets being generally hard to access. * Data residing in various databases. * Variant and exposure/phenotype data not being comparable across studies. Participants in the workshop discussed options for dealing with these challenges, along with their costs and tradeoffs. Videos and accompanying slides from the workshop are available. Also available as a video playlist on GenomeTV | genome, sequencing |
is listed by: OMICtools has parent organization: National Human Genome Research Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_003205 | SciCrunch Registry | 2026-09-26 02:21:42 | 0 |
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