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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VAGUE Resource Report Resource Website 1+ mentions |
VAGUE (RRID:SCR_005607) | VAGUE | software resource | An open-source de novo genome assembly software tool, which is run from the Unix command line, providing a multi-platform graphical front-end for the Velvet de novo assembler. VAGUE is implemented in JRuby and targets the Java Virtual Machine. | command line, assembler |
is listed by: OMICtools has parent organization: Monash University; Melbourne; Australia |
PMID:23162059 | GNU General Public License, v2, Acknowledgement requested | OMICS_00897 | SCR_005607 | Velvet Assembler Graphical Front End | 2026-07-25 12:06:09 | 5 | ||||||
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Bismark Resource Report Resource Website 1000+ mentions |
Bismark (RRID:SCR_005604) | Bismark | software resource | Software tool to map bisulfite converted sequence reads and determine cytosine methylation states. Flexible aligner and methylation caller for Bisulfite-Seq applications. Used to map bisulfite treated sequencing reads to genome of interest and perform methylation calls in single step. | Map bisulfite treated sequence reads, determine cytosine methylation states, genome, sequence reads, perform methylation calls, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Babraham Institute |
PMID:21493656 DOI:10.1093/bioinformatics/btr167 |
Free, Available for download, Freely available | biotools:bismark, OMICS_00575 | https://github.com/FelixKrueger/Bismark, https://bio.tools/bismark | https://sources.debian.org/src/bismark/ | SCR_005604 | 2026-07-25 12:06:09 | 1123 | |||||
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jMHC Resource Report Resource Website 10+ mentions |
jMHC (RRID:SCR_005605) | jMHC | software resource | Software for analyzing and visualization of the results of deep amplicon sequencing. | matlab |
is listed by: OMICtools has parent organization: Google Code |
PMID:21676201 | GNU General Public License, v3, Acknowledgement requested | OMICS_00300 | SCR_005605 | jmhc - software for analyzing and visualization of the results of deep amplicon sequencing | 2026-07-25 12:06:06 | 10 | ||||||
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TMA-Combiner Resource Report Resource Website 1+ mentions |
TMA-Combiner (RRID:SCR_005600) | TMA-Combiner | software resource | A Simple Software Tool to Permit Analysis of Replicate Cores on Tissue Microarrays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | tissue microarray |
is listed by: OMICtools is related to: Stanford TMA Software has parent organization: Stanford University; Stanford; California |
PMID:16258508 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00822 | SCR_005600 | 2026-07-25 12:06:07 | 1 | |||||||
|
TMAJ Resource Report Resource Website 10+ mentions |
TMAJ (RRID:SCR_005601) | TMAJ | software resource | Open-source software to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program. | tissue microarray, java, java swing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA has parent organization: SourceForge |
GNU General Public License, v3 | biotools:tmaj, OMICS_00823 | https://bio.tools/tmaj | SCR_005601 | TMAJ Software Project | 2026-07-25 12:06:09 | 10 | ||||||
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GOProfiler Resource Report Resource Website 1+ mentions |
GOProfiler (RRID:SCR_005683) | GOProfiler | service resource | Service that provides a summary of GO annotations available for each species. The user provides a taxon id and GOProfiler displays the number of GO associations and the number of annotated proteins for that species. The results are listed by evidence code and a separate list of unannotated proteins is also provided. | ontology or annotation browser, annotation, protein, gene ontology |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: AgBase |
PMID:16961921 | Free for academic use | OMICS_02269, nlx_149127 | SCR_005683 | 2026-07-25 12:06:08 | 2 | |||||||
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National Hellenic Research Foundation Resource Report Resource Website 1+ mentions |
National Hellenic Research Foundation (RRID:SCR_005719) | NHRF | institution | The National Hellenic Research Foundation (NHRF) is a multidisciplinary Research Centre established by Royal Decree on 9th October 1958. Its purpose is the organisation, finance and support of high-level research projects in the humanities and the natural sciences. The Humanities Institute cover a wide spectrum of study and research fields in Greek history and culture, contributing substantially and critically to the knowledge and promotion of Greek identity. The Natural Sciences Institutes perform basic and applied research in leading edge areas of science such as health, pharmaceuticals, environment, biotechnology and new materials. They develop innovative methods for solving complex problems facing Greek industry and they provide specialised services and know-how both to the public and private sector. The NHRF is governed by the Board of Directors and the Central Administration under the Director/Chairman of the Board. | humanities, natural sciences | is parent organization of: StRAnGER | ISNI: 0000 0001 2232 6894, grid.22459.38, Wikidata: Q1248816, nlx_149177 | https://ror.org/033m02g29 | SCR_005719 | National Hellenic Research Foundation | 2026-07-25 12:06:09 | 4 | |||||||
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Stanford TMA Software Resource Report Resource Website 1+ mentions |
Stanford TMA Software (RRID:SCR_005598) | Stanford TMA | software resource | Software Tools for High-Throughput Analysis and Archiving of Immunohistochemistry Staining Data Obtained with Tissue Microarrays. | tissue microarray |
is listed by: OMICtools is related to: TMA-Combiner has parent organization: Stanford University; Stanford; California |
PMID:12414504 | OMICS_00819 | SCR_005598 | Stanford TMA Software website, Stanford Tissue Microarray Software | 2026-07-25 12:06:06 | 1 | |||||||
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OXBench Resource Report Resource Website 1+ mentions |
OXBench (RRID:SCR_005591) | OXBench | software resource | A suite of programs aimed at developers of alignment methods rather than end-users to assess the accuracy of multiple sequence alignment methods. It includes a reference database of protein multiple sequence alignments that were generated by consideration of protein three-dimensional structure. | alignment, linux, protein, sequence alignment |
is listed by: OMICtools has parent organization: University of Dundee; Scotland; United Kingdom |
PMID:14552658 | Acknowledgement requested | OMICS_00983 | http://www.compbio.dundee.ac.uk/Software/Oxbench/oxbench.html Alt. URL: http://www.compbio.dundee.ac.uk/software.html | SCR_005591 | 2026-07-25 12:06:09 | 2 | ||||||
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Staden Package Resource Report Resource Website 50+ mentions |
Staden Package (RRID:SCR_005629) | software resource | A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows. | c, unix/linux, sequence assembly, dna/protein analysis, spin, sequence alignment, genome, genome viewer, c++, fortran, tcl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20513662 DOI:10.1093/bioinformatics/btq268 |
BSD License | OMICS_00894, biotools:staden | https://bio.tools/staden, https://sources.debian.org/src/staden/ | SCR_005629 | Staden Package | 2026-07-25 12:06:06 | 79 | ||||||
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Chromaseq Resource Report Resource Website 1+ mentions |
Chromaseq (RRID:SCR_005587) | Chromaseq | software resource | A software package in Mesquite that processes chromatograms, makes contigs, base calls, etc., using in part the programs Phred and Phrap. | chromatogram, sequence, mesquite |
is listed by: OMICtools has parent organization: Oregon State University; Oregon; USA |
NSF EF-0531754 | Acknowledgement required | OMICS_01017 | SCR_005587 | Chromaseq: a package for processing chromatograms and sequence data in Mesquite | 2026-07-25 12:06:09 | 7 | ||||||
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snp-search Resource Report Resource Website |
snp-search (RRID:SCR_005618) | snp-search | software resource | A software tool that manages SNP data and outputs useful information which can be used to test important biological hypotheses. | is listed by: OMICtools | PMID:24246037 | OMICS_00303 | SCR_005618 | 2026-07-25 12:06:09 | 0 | |||||||||
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Burroughs Wellcome Fund Resource Report Resource Website 100+ mentions |
Burroughs Wellcome Fund (RRID:SCR_005772) | BWF | institution | The Burroughs Wellcome Fund is an independent private foundation dedicated to advancing the biomedical sciences by supporting research and other scientific and educational activities. Within this broad mission, BWF has two primary goals: * To help scientists early in their careers develop as independent investigators * To advance fields in the basic biomedical sciences that are undervalued or in need of particular encouragement BWF''s financial support is channeled primarily through competitive peer-reviewed award programs. * BWF''s endowment: $586.8 million at the end of FY 2009 * BWF approved $26.4 million in grants during FY 2009 BWF makes grants primarily to degree-granting institutions on behalf of individual researchers, who must be nominated by their institutions. To complement these competitive award programs, BWF also makes grants to nonprofit organizations conducting activities intended to improve the general environment for science. A Board of Directors comprising distinguished scientists and business leaders governs BWF. BWF was founded in 1955 as the corporate foundation of the pharmaceutical firm Burroughs Wellcome Co. In 1993, a generous gift from the Wellcome Trust in the United Kingdom, enabled BWF to become fully independent from the company, which was acquired by Glaxo in 1995. BWF has no affiliation with any corporation. | biomedical sciences, research, science, education | Wellcome Trust | nlx_149371, grid.427464.7, Wikidata: Q5000488, ISNI: 0000 0000 8727 8697, Crossref funder ID: 100000861 | https://ror.org/01d35cw23 | SCR_005772 | 2026-07-25 12:06:12 | 103 | ||||||||
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CSIBS Resource Report Resource Website |
CSIBS (RRID:SCR_005889) | CSIBS | software resource | A software tool designed to aid researchers in browsing through scientific literature. As one reads an online article and encounters a citation that looks important, CSIBS creates a preview summary of the cited document. The key innovation is the contextual tailoring of the automatically generated summaries using the citation and its surrounding text. As this context changes, so too does the citation-specific summary portion of the preview, which contains contextually-relevant sentences extracted from the cited document. The CSIBS preview presents relevant information required to appraise the citation, containing meta-data about the reference, the abstract and the citation-specific summary. Thus, CSIBS, alleviates information overload by enabling the reader to determine whether or not to invest time in exploring the cited article further. Reference, http://www.sciencedirect.com/science/article/pii/S1570826810000181 | elsevier grand challenge, natural language processing, text summarization, document browsing aid, contextual summary, computational linguistics, text mining, metadata |
is listed by: FORCE11 has parent organization: ICT Centre has parent organization: Macquarie University; Sydney; Australia |
Prototype | nlx_149460 | http://www.force11.org/node/4689 | SCR_005889 | CSIBS: The Citation-Sensitive In-Browser Summarizer, Citation-Sensitive In-Browser Summarizer | 2026-07-25 12:06:11 | 0 | ||||||
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GlycoPeptideSearch Resource Report Resource Website |
GlycoPeptideSearch (RRID:SCR_005767) | GPS | software resource | GlycoPeptideSearch (GPS) simplifies data interpretation of N-glycopeptide CID MS/MS datasets by searching for glycopeptide results consistent with MS/MS spectra. Results are tabulated in Excel format. Accelerate and simplify interpretation of N-glycopeptide CID MS/MS spectra using GlycoPeptideSearch (GPS). This tool is designed for tandem mass-spectra acquired from proteolytic digests of purified glycoproteins modified with N-glycans and analyzed by LC-MS/MS and CID. The search yields an Excel spreadsheet of N-glycopeptide matches consistent with the spectra. GPS requires two files as input - an mzXML (or other open spectral format) file of glycopeptide CID tandem mass-spectra and a text file (.txt) of peptide sequences containing the N-linked glycosylation motif NXS/T. Spectral datafiles must be converted from raw vendor formats, such as .RAW or .wiff, to an open peak list format (mzXML preferred). In addition to these two input files, the user must specify one or more glycan databases (provided in the software package). The database(s) selected by the user will be used to match glycan structures in the glycopeptide spectra. The output is an Excel spreadsheet with one or more rows for spectra within the dataset that contain evidence of glycoprotein fragmentation, paired with one or more proposed glycopeptide matches for each spectrum. Glycopeptide matches consist of a peptide-glycan pair, with the peptide drawn from the user-supplied peptide file, and the glycan selected from a glycan database(s). The human subset of the GlycomeDB glycan database is provided, and N-linked glycans are automatically selected from it. GPS interprets glycopeptide CID MS/MS spectra by first requiring MS/MS spectra contain evidence of glycopeptide fragmentation - the oxonium ion peaks (m/z 204 - Hex, m/z 366 - HexNAc), and N-glycopeptide core specific peaks (peptide, peptide + HexNAc, peptide + HexNAc-HexNAc, peptide + HexNAc-HexNAc-Hex). For spectra that meet these initial criteria, for a particular peptide, a mass-based search of one or more glycan databases looks for glycans which capture the remaining mass of the spectral precursor. Additional spectral information may be used to narrow the number of matches, and equivalent glycan topologies may be collapsed to a single peptide-glycan pair. GPS also provides N-glycan compositions with the necessary additional mass, even if no glycan with the composition is present in the glycan database(s). GPS can either be run from the command-line or by using its graphical user interface. We recommend the msconvert (or MSConvertGUI) software from the ProteoWizard project to convert spectral datafiles from vendor formats such as .wiff and .RAW into mzXML. | peptide, glyopeptide, glycoprotein, mass-spectra, ms/ms spectra | has parent organization: Edwards Lab | PMID:22239659 | nlx_149231 | SCR_005767 | 2026-07-25 12:06:09 | 0 | ||||||||
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Finnish Cancer Registry Resource Report Resource Website 1+ mentions |
Finnish Cancer Registry (RRID:SCR_005881) | Finnish Cancer Registry | institution | The Finnish Cancer Registry maintains a nation-wide database on all cancer cases in Finland going back to 1953. It is also an internationally active institute for statistical and epidemiological cancer research. The Mass Screening Registry is a department of the Finnish Cancer Registry, and is responsible of planning and evaluating national cancer screening programs in Finland. The site contains information on cancer research and up to date statistics on the prevalence of different types of cancer in Finland, the Nordic countries and on a global level. The web pages include information for participants in cancer screening and for professionals involved in organizing such screening. | Cancer | Cancer Society of Finland | grid.424339.b, nlx_149446, ISNI: 0000 0000 8634 0612 | https://ror.org/00j15sg62 | SCR_005881 | 2026-07-25 12:06:13 | 8 | ||||||||
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MAGMA Resource Report Resource Website 100+ mentions |
MAGMA (RRID:SCR_005757) | MAGMA | software resource | Software that utilizes a multiobjective evolutionary algorithm for genetic mapping. It is based on a the ECJ evolutionary software package written by Sean Luke and includes the Strength Pareto Evoluationary Algorithm Version 2 changes for multiobjective analysis. The code runs on any platform with Java Version 2. A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers. These genetic markers occur at discrete positions along the genome, which is a collection of one or more linear chromosomes. Typing the value of a marker in an individual carries a cost; one seeks to minimize the number of markers typed without excessively jeopardizing the probability of detecting an association between a marker and a disease phenotype. MAGMA is a project which employ''s a multiobjective evolutionary algorithm to solve this problem. | gene, genetic mapping, algorithm, genomics, single nucleotide polymorphism, population study, haplotype-block elucidation, java | has parent organization: SourceForge | Juvenile Diabetes Research Foundation | PMID:12875658 | Open unspecified license | nlx_149220 | SCR_005757 | Multiobjective Analyzer for Genetic Marker Acquisition, MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition | 2026-07-25 12:06:11 | 456 | |||||
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Icahn School of Medicine at Mount Sinai; New York; USA Resource Report Resource Website 1+ mentions |
Icahn School of Medicine at Mount Sinai; New York; USA (RRID:SCR_005793) | ISMMS, MSSM | university | Icahn School of Medicine at Mount Sinai, formerly Mount Sinai School of Medicine, is graduate medical school in Manhattan, New York City. Leader in medical and scientific training and education, biomedical research and patient care. | medicine, medical, school, university, doctorate, phd |
uses: Scizzle is affiliated with: BioJupies is related to: Alzheimers Disease Genetics Consortium is related to: Beta Cell Biology Consortium is related to: Clinical and Translational Science Awards Consortium is related to: proMODMatcher is parent organization of: Enrichr is parent organization of: Neuropathology of CTE and Delayed Effects of TBI: Toward In-Vivo Diagnostics is parent organization of: NeuronStudio is parent organization of: Rayburst Open-Source Code is parent organization of: Volume Integration and Alignment System is parent organization of: Volume Integration and Alignment System Source Code is parent organization of: NeuroGL is parent organization of: TIFF Stack Sub-Sampler is parent organization of: Cre-X-Mice: A Database of Cre Transgenic Lines is parent organization of: Mount Sinai School of Medicine: In-Vivo Molecular Imaging Laboratory is parent organization of: Mount Sinai Biobank is parent organization of: ChEA is parent organization of: Kismeth is parent organization of: Lists2Networks is parent organization of: Mount Sianai Department of Neuroscience is parent organization of: NetworKIN is parent organization of: Mount Sinai Alzheimer's Disease Research Center is parent organization of: Manhattan HIV Brain Bank is parent organization of: Computational Neurobiology and Imaging Center is parent organization of: L1000 Characteristic Direction Signature Search Engine is parent organization of: L1000 Fireworks Display is parent organization of: Drug Gene Budger is parent organization of: COVID-19 Crowd Generated Gene and Drug Set Library is parent organization of: GeneOverlap is parent organization of: Datanator is parent organization of: BioSimulations is parent organization of: DE-Sim is parent organization of: Appyters is parent organization of: ezTrack project is parent organization of: Minian is parent organization of: TargetRanger is parent organization of: GeneRanger is parent organization of: Kinase Enrichment Analysis 3 is parent organization of: X2K Web is parent organization of: Diabetes Data and Hypothesis Hub is parent organization of: Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Transgenic and Genome Editing Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Stem Cell Engineering Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Metabolomics Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Neuropathology Brain Bank and Research CoRE Facility is parent organization of: Icahn School of Medicine at Mount Sinai RNA Nanocore Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Human Immune Monitoring Center Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Center for Advanced Genomics Technology Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Biorepository and Pathology Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Mount Sinai Cryo-EM CoRE Core Facility |
nlx_55912, grid.59734.3c, Crossref funder ID:100007277, ISNI:0000 0001 0670 2351, Wikidata:Q1950740 | https://ror.org/04a9tmd77 | SCR_005793 | Mount Sinai School of Medicine, Icahn School of Medicine, Icahn School of Medicine at Mount Sinai | 2026-07-25 12:06:12 | 6 | |||||||
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SPLINTER Resource Report Resource Website 10+ mentions |
SPLINTER (RRID:SCR_005826) | SPLINTER | software resource | Software that detects and quantifies short IN/DELs as well as single nucleotide substitutions in pooled-DNA samples. |
is listed by: OMICtools has parent organization: Washington University in St. Louis; Missouri; USA |
Cancer | Free for academic / non-profit use, Commercial use requires license | OMICS_00100 | SCR_005826 | Short IN/DEL Prediction by Large deviation Inference and Non-linear True frequency Estimation by Recursion | 2026-07-25 12:06:09 | 13 | |||||||
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GOEx - Gene Ontology Explorer Resource Report Resource Website 10+ mentions |
GOEx - Gene Ontology Explorer (RRID:SCR_005779) | GOEx | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. Gene Ontology Explorer (GOEx) combines data from protein fold changes with GO over-representation statistics to help draw conclusions in proteomic experiments. It is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alternative strategy, there will be no protein fold information. Platform: Windows compatible | proteomics, visualization, statistical analysis, gene ontology, parse, pattern recognition, spectral counting, analysis, protein fold |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Scripps Research Institute |
CNPq ; CAPES ; FAPERJ BBP grant ; PAPES ; PDTIS ; Ary Frauzino Foundation ; NIAID ; NIH ; genesis molecular biology laboratory ; Fiocruz-INCA collaboration ; NIAID UCSD/MCB0237059; NCRR P41RR011823; NIMH 5R01 MH067880 |
PMID:19239707 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149249 | http://pcarvalho.com/patternlab/goex.shtml | SCR_005779 | Gene Ontology Explorer, GO Explorer | 2026-07-25 12:06:12 | 26 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
