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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SplicePlot Resource Report Resource Website |
SplicePlot (RRID:SCR_001172) | SplicePlot | software resource | A software tool for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. It provides a simple command line interface for drawing sashimi plots, hive plots, and structure plots of alternative splicing events from .bam, .gtf, and .vcf files. | visualization, alternative splicing, splicing quantitative trait loci, quantitative trait loci, rna-seq, hive plot, structure plot, sashmi plot, python, linux, mac os, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University School of Medicine; California; USA |
PMID:24363378 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02185, biotools:spliceplot | https://bio.tools/spliceplot | SCR_001172 | SciCrunch Registry | SplicePlot: a tool for visualizing alternative splicing | 2026-09-26 02:12:55 | 0 | |||||
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ChIPsim Resource Report Resource Website 1+ mentions |
ChIPsim (RRID:SCR_001293) | ChIPsim | software resource | Software package providing a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments. | chip-seq, infrastructure, simulation |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or newer | OMICS_02042 | SCR_001293 | SciCrunch Registry | ChIPsim - Simulation of ChIP-seq experiments | 2026-09-26 02:12:57 | 1 | |||||||
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methyAnalysis Resource Report Resource Website 1+ mentions |
methyAnalysis (RRID:SCR_001290) | methyAnalysis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focuses on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data. | dna methylation, microarray, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21159174 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02046 | SCR_001290 | SciCrunch Registry | methyAnalysis - DNA methylation data analysis and visualization | 2026-09-26 02:12:57 | 9 | ||||||
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WiggleTools Resource Report Resource Website 1+ mentions |
WiggleTools (RRID:SCR_001170) | WiggleTools | data processing software, software application, software library, software resource, software toolkit | A multithreaded software library that computes statistics on large numbers of datasets, generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions. | visualization, statistical analysis, parallel processing, genome |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
PMID:24363377 | Apache License, v2 | OMICS_02188 | SCR_001170 | SciCrunch Registry | 2026-09-26 02:12:55 | 2 | |||||||
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les Resource Report Resource Website |
les (RRID:SCR_001291) | les | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes. | loci of enhanced significance, tiling microarray, tiling, microarray, chip-chip, dna modification, probe, dna methylation, differential expression, microarray, transcription, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:les, OMICS_02045 | https://bioconductor.org/packages/les/, https://bio.tools/les | SCR_001291 | SciCrunch Registry | les package: Identifying Differential Effects in Tiling Microarray Data, Loci of Enhanced Significance | 2026-09-26 02:12:57 | 0 | ||||||
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GVK Biosciences Labs and Facilities Resource Report Resource Website |
GVK Biosciences Labs and Facilities (RRID:SCR_001044) | access service resource, core facility, data or information resource, portal, service resource | A contract research organization based in India that provides services including Clinical Development, Contract Manufacturing and Informatics. | contract research organization, India, informatics, commercial |
is listed by: ScienceExchange is related to: GVK BIO Chemistry Group |
THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_4904 | SCR_001044 | SciCrunch Registry | GVK Biosciences Labs & Facilities | 2026-09-26 02:12:54 | 0 | ||||||||
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Bleeding History Phenotype Ontology Resource Report Resource Website |
Bleeding History Phenotype Ontology (RRID:SCR_001165) | BHO | controlled vocabulary, data or information resource, ontology | An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders. | owl | is listed by: BioPortal | Hemorrhagic disorder | nlx_157338 | SCR_001165 | SciCrunch Registry | 2026-09-26 02:12:55 | 0 | ||||||||
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International Essential Tremor Foundation Resource Report Resource Website |
International Essential Tremor Foundation (RRID:SCR_001163) | IETF | institution | The IETF is an international nonprofit organization whose mission is to provide global educational information, services and support to those affected by essential tremor (ET) and to health care providers, while promoting and funding ET research. Services provided by the IETF include mailing or emailing a free information packet about ET upon request, maintaining an up-to-date listing of physicians specializing in ET, and assisting in forming and maintaining ET support groups. In addition, the IETF conducts several free educational events in cities across the United States every year, and an annual awareness campaign that runs in conjunction with the organization's largest fundraising activity, Tulips for Tremors. Every year, the IETF also funds basic research into the cause(s) of ET. Small grants are awarded to established scientists whose primary interest is tremor disorders. The IETF funds this program in the hope that these scientists will collect sufficient published data to help them qualify for future federal funding that will lead to better treatments and a cure. IETF members receive two copies a year of the member magazine, Tremor Talk and three copies of the research newsletter, The Scoop on Tremor. Articles in both publications are written for the non-medically trained person and discuss recent advances in research, coping techniques and topics of general interest to those with ET. Medical and research articles are written by physicians and researchers who work with patients with ET and/or study ET in laboratories. The International Essential Tremor Foundation is based in Lenexa, Kansas. | essential tremor, essential tremor online community, essential tremor organization, tremor, tremor research, tremor research funding | Crossref funder ID: 100008447, ISNI: 0000 0004 5903 8599, nif-0000-11649, grid.480535.f | https://ror.org/005vegy94 | http://essentialtremor.xportcms9.com/Home | SCR_001163 | SciCrunch Registry | 2026-09-26 02:12:55 | 0 | ||||||||
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MetaPhyl Resource Report Resource Website |
MetaPhyl (RRID:SCR_001169) | MetaPhyl | software resource | Software implementing a supervised classification method for metagenomic samples that takes advantage of the natural structure of microbial community data encoded by phylogenetic trees. | c++, linux, mac osx, phylogenetic tree, command line, classification, metagenomic |
is listed by: OMICtools has parent organization: University of California at Riverside; California; USA |
PMID:24369151 | Free, Available for download, Freely available | OMICS_02189 | SCR_001169 | SciCrunch Registry | 2026-09-26 02:12:55 | 0 | |||||||
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Ottawa Hospital Research Institute Labs and Facilities Resource Report Resource Website |
Ottawa Hospital Research Institute Labs and Facilities (RRID:SCR_001045) | OHRI Labs and Facilities, OHRI Labs & Facilities | access service resource, core facility, data or information resource, portal, service resource | Portal to research facilities and services within the Ottawa Hospital Research Institute. Facilities and services include access to their bioinformatics facility, flow cytometry facility, human pluripotent stem cell facility, and their clinical research lab. | genomics, proteomics, biotechnology, bioinformatics, human health, ottawa, research service |
is listed by: ScienceExchange has parent organization: University of Ottawa; Ontario; Canada |
THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_4969 | http://www.scienceexchange.com/facilities/4969 | SCR_001045 | SciCrunch Registry | , Research Institute Labs, Ottawa Hospital, Facilities, OHRI | 2026-09-26 02:12:54 | 0 | ||||||
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icyou Health Videos Resource Report Resource Website |
icyou Health Videos (RRID:SCR_001167) | data or information resource, portal, topical portal, video resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. icyou is an internet resource of health-related video clips submitted by users. Health topics covered in videos can range anywhere from infectious diseases to fitness and exercise, with videos generally being shorter than 10 minutes in length. Videos also contain information on treatment and procedures, medical fields, and health politics and policy. These videos may or may not be authored by licensed medical personnel. All videos are searchable, and users can also choose to upload their own healthcare-related videos. In addition to gathering healthcare video from the best sources on the Web and beyond, icyou.com can call on its own award-winning health reporting team to cover the latest issues and trends. Through its parent company Benefitfocus, icyou.com has full access to the Benefitfocus Media Studio, a state-of-the-art HD facility located in Charleston, South Carolina. This studio is the only one of its kind devoted solely to creating healthcare-oriented video content. In it, the Benefitfocus Media team creates up-to-the-minute reports, tutorials, features and more that help illuminate its users about the complexities of the many facets of healthcare. | exercise, fitness, healthcare, health policy, health politics, health topic, medical fields, medical procedure, treatment | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-11652 | http://www.icyou.com | SCR_001167 | SciCrunch Registry | icyou | 2026-09-26 02:12:55 | 0 | ||||||||
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beadarraySNP Resource Report Resource Website |
beadarraySNP (RRID:SCR_001281) | beadarraySNP | software resource | Software package for importing data from Illumina SNP experiments and performing copy number calculations and reports. | copy number variation, data import, genetic variability, preprocessing, snp, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02056 | http://www.bioconductor.org/packages/devel/bioc/html/beadarraySNP.html | SCR_001281 | SciCrunch Registry | beadarraySNP - Normalization and reporting of Illumina SNP bead arrays | 2026-09-26 02:12:57 | 0 | ||||||
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Transposon Insertion Finder Resource Report Resource Website 1+ mentions |
Transposon Insertion Finder (RRID:SCR_001159) | TIF | software resource | A search program to detect insertions of transposable element from short reads of next generation sequencer. | perl, unix/linux | is listed by: OMICtools | PMID:24629057 | Free, Available for download, Freely available | OMICS_03508 | SCR_001159 | SciCrunch Registry | Transposon Insertion Finder | 2026-09-26 02:12:55 | 1 | ||||||
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Baa.pl Resource Report Resource Website |
Baa.pl (RRID:SCR_001197) | Baa.pl | software resource | Software tool to evaluate de novo genome assemblies with RNA transcripts. | genomics, genome assembly, rna transcript, perl | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02154 | https://github.com/josephryan/baa.pl | SCR_001197 | SciCrunch Registry | 2026-09-26 02:12:56 | 0 | |||||||
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Medical College of Wisconsin; Wisconsin; USA Resource Report Resource Website |
Medical College of Wisconsin; Wisconsin; USA (RRID:SCR_001077) | MCW | university | Private and freestanding medical school and graduate school of sciences in Milwaukee, Wisconsin. The institution offers medical degrees as well as masters and PhD-level studies in areas such as biochemistry, cell biology, and community and public health. | private, freestanding, medical, graduate, masters, phd, public health, university |
is related to: Clinical and Translational Science Awards Consortium is parent organization of: Clinical Measurement Ontology is parent organization of: Experimental Conditions Ontology is parent organization of: RatMine is parent organization of: Rat Genome Database (RGD) is parent organization of: Medical College of Wisconsin Cell Biology Neurobiology and Anatomy is parent organization of: National Biomedical Electron Paramagnetic Resonance Center is parent organization of: Cytopathology Foundation is parent organization of: Rat Genome Database: Neurological Disease Portal is parent organization of: Flash Gviewer is parent organization of: Medical College of Wisconsin Mellowes Center for Genomic Sciences and Precision Medicine Core Facility is parent organization of: Medical College of Wisconsin Oxford Instruments Center for Advanced Microscopy Electron Microscopy Core Facility is parent organization of: Medical College of Wisconsin Cancer Center Geospatial, Epidemiology and Outcomes Shared Resource Core Facility is parent organization of: Medical College of Wisconsin Echo Core Shared High-Frequency Ultrasound Imaging Core Facility is parent organization of: Medical College of Wisconsin Tissue Bank is parent organization of: Medical College of Wisconsin Translational Metabolomics Shared Resource Mass Spectrometry Core Facility is parent organization of: Medical College of Wisconsin Cancer Center Structural Biology Shared Resource Core Facility is parent organization of: Medical College of Wisconsin Cancer Center Translational Metabolomics Shared Resource, Redox and Bioenergetics Core Facility is parent organization of: Medical College of Wisconsin Cancer Center Cell Therapy Shared Resource Core Facility is parent organization of: Medical College of Wisconsin Children’s Research Institute CRI Imaging Core Facility is parent organization of: Medical College of Wisconsin Neuroscience Research Center NRC Microscopy Core Facility is parent organization of: Medical College of Wisconsin Comprehensive Rodent Metabolic Phenotyping Core Facility is parent organization of: Medical College of Wisconsin Children's Research Institute Histology Core Facility is parent organization of: Medical College of Wisconsin MCW Engineering Core Facility is parent organization of: Medical College of Wisconsin Cancer Center Stem Cell and Organoid Core Facility is parent organization of: Medical College of Wisconsin Cancer Center Biostatistics Shared Resource Core Facility is parent organization of: Medical College of Wisconsin Children's Research Institute Flow Cytometry Core Facility is parent organization of: Medical College of Wisconsin Center for Microbiome Research Core Facility is parent organization of: Medical College of Wisconsin Cardiovascular Research Center CVRC Microscopy Core Facility is parent organization of: Medical College of Wisconsin Center for Imaging Research Core Facility |
, GRID grid.30760.32, ISNI 0000 0001 2111 8460, nlx_30873, Crossref Funder ID 100008980, Wikidata Q6806307 | https://ror.org/00qqv6244 | SCR_001077 | SciCrunch Registry | Medical College of Wisconsin | 2026-09-26 02:12:54 | 0 | |||||||
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VirusHunter Resource Report Resource Website |
VirusHunter (RRID:SCR_001198) | VirusHunter | software resource | A fully automated and modular software package for mining sequence data to identify sequences of microbial origin. The pipeline was optimized for analysis of data generated by the Roche/454 next-generation sequencing platform but can be applied to longer sequences (Sanger sequencing data or assembled contigs) as well. Microbial sequences are identified on the basis of BLAST alignments and the taxonomic classification of the reference sequence(s) to which a read is aligned. Viruses are the focal point of VirusHunter as released, but it can be easily modified to generate parallel outputs for bacterial or parasitic species. To date, VirusHunter has been applied to thousands of specimens, including human, animal and environmental samples, resulting in the detection of many known and novel viruses. | virus, next-generation sequencing, roche, 454, taxonomic classification, alignment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:24167629 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:virushunter, OMICS_02153 | https://bio.tools/virushunter | SCR_001198 | SciCrunch Registry | 2026-09-26 02:12:56 | 0 | ||||||
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University of Oklahoma; Oklahoma; USA Resource Report Resource Website 1+ mentions |
University of Oklahoma; Oklahoma; USA (RRID:SCR_001074) | OU | university | A coeducational public research university located in Oklahoma, USA. The institution confers undergraduate and graduate degrees in fields such as law, medicine, aviation, energy management, history of science, and Native American studies. | public, research, university, undergraduate, graduate |
is parent organization of: Development of a Specific-Pathogen-Free Baboon Colony is parent organization of: University of Oklahoma College of Medicine; Oklahoma; USA is parent organization of: Amblyomma Americanum (Lone Star Tick) cDNA Sequencing is parent organization of: Baboon Research Resouces is parent organization of: Cryptococcus Neoformans cDNA Sequencing is parent organization of: University of Oklahoma Labs and Facilities is parent organization of: University of Oklahoma Health Sciences Center Laboratory for Molecular Biology and Cytometry Research Core Facility is parent organization of: University of Oklahoma Samuel Roberts Nobel Microscopy Laboratory Core Facility is parent organization of: University of Oklahoma Health Sciences Center OK INBRE Data Science Core Facility is parent organization of: University of Oklahoma Protein Production and Characterization Core Facility is parent organization of: University of Oklahoma Biomolecular Structure Core Facility is parent organization of: University of Oklahoma Health Sciences Center Tissue Pathology and Biospecimen Core Facility is parent organization of: University of Oklahoma College of Medicine Immunology and Informatics Core Facility is parent organization of: University of Oklahoma Health Sciences Center Ocular Immunobiology Core Facility is parent organization of: University of Oklahoma Health Sciences Live Animal Imaging and Analysis Core Facility is parent organization of: University of Oklahoma Health Sciences Center Cellular Imaging and Morphometric Analysis Core Facility |
nlx_27458, grid.266900.b, Wikidata:Q640652, ISNI:0000 0004 0447 0018, Crossref funder ID:100007926 | https://ror.org/02aqsxs83 | SCR_001074 | SciCrunch Registry | University of Oklahoma | 2026-09-26 02:12:54 | 1 | |||||||
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University of Adelaide; Adelaide; Australia Resource Report Resource Website 1+ mentions |
University of Adelaide; Adelaide; Australia (RRID:SCR_001075) | university | Public research university in Adelaide, South Australia. It is known for its focus on research and emphasis on moving towards commercialization of research. | public, research, university, adelaide, australia, research, commercialization |
is parent organization of: Neural Network Resources is parent organization of: Centre for Automotive Safety Research |
Wikidata:Q15574, nlx_73637, ISNI:0000 0004 1936 7304, Crossref funder ID:501100001786, grid.1010.0 | https://ror.org/00892tw58 | SCR_001075 | SciCrunch Registry | 2026-09-26 02:12:54 | 2 | |||||||||
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Athens Research and Technology Resource Report Resource Website 1+ mentions |
Athens Research and Technology (RRID:SCR_001079) | commercial organization | Commercial supplier of bioproducts for studies of inflammation, autoimmune disease, cancer, coronary disease, Alzheimer's Disease and more. These include antibodies, enzymes, coagulation factors, and assay kits. | antibody, protein, biotherapeutics, autoimmune disease, cancer, coronary disease, alzheimers disease | inflammation, autoimmune disease, cancer, coronary disease, Alzheimer's Disease | Wikidata: Q30284050, nlx_152285, grid.423006.3 | https://ror.org/0527dhk70 | SCR_001079 | SciCrunch Registry | Athens Research and Technology Inc. | 2026-09-26 02:12:54 | 1 | ||||||||
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bsseq Resource Report Resource Website 1+ mentions |
bsseq (RRID:SCR_001072) | data analysis software, data processing software, sequence analysis software, software application, software resource | R package with tools for analyzing and visualizing bisulfite sequencing data. | bisulfite sequencing, analyze, r, sequence analysis software, data analysis software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01847, biotools:bsseq | https://bio.tools/bsseq | SCR_001072 | SciCrunch Registry | bsseq - Analyze manage and store bisulfite sequencing data | 2026-09-26 02:12:54 | 8 |
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