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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Howard University; Washington D.C. Resource Report Resource Website |
Howard University; Washington D.C. (RRID:SCR_001084) | HU | university | A federally chartered, private, coeducational, nonsectarian, historically black university in Washington, D.C. Howard University has graduate schools in many fields, including business, nursing, engineering, and medicine. | undergraduate, graduate, master's, doctoral, phD, institution, university, nonsectarian |
is related to: Clinical and Translational Science Awards Consortium is parent organization of: Howard Flow Cytometry Core is parent organization of: Howard Imaging Core Facility: Molecular Imaging Laboratory is parent organization of: Howard Biobehavioral Core Laboratory is parent organization of: Howard Biostatistics Core is parent organization of: Howard University Center for Computational Biology and Bioinformatics Core Facility is parent organization of: Howard Molecular Genetics Core is parent organization of: Howard Nanoscale Science and Engineering Facility is parent organization of: Howard RCMI Proteomics Facility |
nlx_152178 | SCR_001084 | Howard, Howard University, Howard U | 2026-09-03 04:44:13 | 0 | ||||||||
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University of Florida College of Medicine Neuroscience Resource Report Resource Website |
University of Florida College of Medicine Neuroscience (RRID:SCR_001081) | data or information resource, department portal, organization portal, portal | A department at the University of Florida's College of Medicine that offers programs of study on neural function and how it changes with injury and disease. The institution's research ranges from fundamental discovery to clinical application. These neuroscience programs are offered at the undergraduate, graduate, postdoctoral and resident level. | neuroscience, neural function, undergraduate, graduate, postdoctoral, resident, clinical, injury, disease | nif-0000-02172 | SCR_001081 | UFL | 2026-09-03 04:44:15 | 0 | ||||||||||
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jmzML Resource Report Resource Website 1+ mentions |
jmzML (RRID:SCR_001119) | software resource | A Java application programming interface (API) for the Proteomics Standards Initiative mzML data standard. | standalone software, mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:20127693 | Free, Available for download, Freely available | biotools:jmzml, OMICS_03340 | https://bio.tools/jmzml | SCR_001119 | 2026-09-03 04:44:23 | 1 | |||||||
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CISCRP- The Center for Information and Study on Clinical Research Participation Resource Report Resource Website |
CISCRP- The Center for Information and Study on Clinical Research Participation (RRID:SCR_001152) | data or information resource, portal, topical portal | CISCRP is a resource for information on participation in, understanding of, and resources for clinical research participants and scientists. The mission of the Center is to educate, inform and empower patients, the public, medical and research professionals, the media and policymakers about clinical research participation and what it means to be an active participant in the clinical research process, promote greater awareness and understanding of clinical research participation and the role that it plays in public health, facilitate more effective collaboration among all members of the clinical research enterprise, and provide resources for the research community to better understand the study volunteer. To that end, the Center has developed a broad national awareness and education initiative in order to better inform the public at large about clinical study information. Furthermore, on its website, the Center offers program and event information related to clinical trials, an information center with facts, figures, informational resources, and FAQs for both patients and researchers, and a mailing list of clinical trial information. :The Center also maintains its own search engine website, : :searchclinicaltrials.org : : :, for those looking for further clinical trial information. The Center for Information and Study on Clinical Research Participation is located in Dedham, MA. :NIF thanks the : :Parkinson's Disease Foundation : : :for their referral of this resource to us. | clinical research, clinical study | nif-0000-11642 | SCR_001152 | CISCRP | 2026-09-03 04:44:25 | 0 | ||||||||||
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massiR Resource Report Resource Website |
massiR (RRID:SCR_001157) | software resource | Software that predicts the sex of samples in gene expression microarray datasets. | standalone software, mac os x, unix/linux, windows, r, classification, clustering, gene expression, microarray, quality control, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24659105 | Free, Available for download, Freely available | biotools:massir, OMICS_03638 | https://bio.tools/massir | SCR_001157 | massiR: MicroArray Sample Sex Identifier, MicroArray Sample Sex Identifier | 2026-09-03 04:44:16 | 0 | ||||||
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CenterWatch Resource Report Resource Website 1+ mentions |
CenterWatch (RRID:SCR_001158) | data or information resource, portal, topical portal | CenterWatch is an online resource for news, directories, analysis, and proprietary market research for clinical research professionals and patients. For patients, CenterWatch is committed to providing information on clinical trials, specific drugs, as well as other essential health and educational resources. On this website, patients can search clinical trials, receive e-mail notifications about specific clinical trials, review results from completed clinical trials, search drug information, learn about volunteering for a clinical trial, read an overview of the clinical trials process and find other health and educational resources. For researchers, CenterWatch offers a wide range of tools and resources to improve patient and investigator recruitment, remain current with industry trends and business practices, and strengthen organizational procedures. CenterWatch also offers information on grant opportunities, and a variety of educational books and publications. Researchers can provide the public with information about their clinical trials by using the Clinical Trials Listing Serviceprovided through CenterWatch, or look up more specific information on medicines and equipment using Drug and Device Pipeline News. Overall, the mission of CenterWatch is to be the leading source of news, directories, analysis, and proprietary market research for clinical research professionals and patients. It is located in Boston, MA. :NIF thanks the :Parkinson's Disease Foundation : :for their referral of this resource to us. | drug information, drug study, clinical research, clinical study, clinical trial, medicine, patient, health, medical | nif-0000-11641 | SCR_001158 | CenterWatch | 2026-09-03 04:44:17 | 9 | ||||||||||
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Intramodal Registration Software Resource Report Resource Website |
Intramodal Registration Software (RRID:SCR_001148) | data analysis software, data processing software, software application, software resource | Software that implements a set of C routines for robust, high-quality registration of two volumes, aligning according to a least-squares criterion which is well-suited to intramodal registration tasks. Programming skills are required to attach the ANSI-C routine to whichever system users have. It is available on Unix, Macintosh, and PC. | intramodal registration, unix, pc, macintosh, programming, c | has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland | Free, Available for download, Freely available | nif-0000-00318 | SCR_001148 | 2026-09-03 04:44:18 | 0 | |||||||||
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NeuroMouse Database Resource Report Resource Website |
NeuroMouse Database (RRID:SCR_001143) | NeuroMouse | atlas, data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17, 2023.Toolbook(tm) based, interactive graphical database which provides structural, molecular, and genetic information on the adult murine nervous system; and its relevance to human neurobiology. This resource is primarily designed as a platform for users to interact, each sharing knowledge on their own area of expertise, which is compiled to a master database. This hypertext atlas presently comprises more than 1000 pages and is designed to provide a flexible integrated resource for the description and discussion of all forms mammalian neurologic data. Version 4.0 of the NeuroMouse program extends the program's basic framework to include a number of areas in modern molecular neurobiology. This system provides an integrated resource for the characterization and description of mammalian neurological data. Major divisions include: Neural Atlas, Molecular Atlas, Genetics/Surgical Lesion Atlas. Neuromouse has been integrated into our strain-specific three dimensional MRI and surgical atlases of the murine CNS. Database contents: Neural Atlas: - Rotational representation of the murine brain. - Neural structures: visual and alphabetic point and click index of neural structures, pathways and systems. - Brain atlas:photographic serial sections in the coronal, sagittal, and horizontal planes (average plate distance - 300 um). Physical brain distances are also provided as are meta-index grids to allow rapid movement between different planes and regions. # Catalog of primary and immortalized neural cells indexed to relevant neural structures. Molecular Atlas: - Index of neurotransmitters: Acetylcholine, GABA, Glutamate, Aspartate, Glycine, Dopamine, Norepinephrine, Epinephrine, Serotonin (synthesis, distribution, degradation, molecular modules, receptors, subunits, agonists, antagonists, gene structure, localization, physical properties and transgenics are indicated for each item). - Index of neurotrophins / neurokines: NGF, BDNF, NT-3, NT-4/5, CNTF, LIF, Onostain M, IL-6, GDNF, FGF's, S100b (ligand, receptors, expression pattern, physical properties, homologous factors, transgenics/knockouts, chromosomal location, effects of agent, and effects of factors on agent are indicated for each item). - Index of additional neural agents: Bcl-2, TNF/Fas, TGF-beta, P53/Rb, PDGF, EGF family (ligand, receptor, expression patterns, physical properties, homologous factors, transgenics/ knockouts, chromosomal location, effects of agent, effects of factors on agent are indicated for each item). - Molecular biology: Molecular biology of important neural genes with integrated l links, plus selected neural topics (ex. programmed cell death, inducible gene systems, protein motifs, neural gene elements, and selected signal transduction pathways). Genetics Atlas: - Lesion paradigms: Index of common neuronal structural and chemical lesion paradigms. - Selected procedures: description of common neurosurgical, cell tracing, culturing and laboratory procedures. - Neurologic syndromes: Index of important human neurologic syndromes and appropriate animals models. - Neural mutant database: Index and description of naturally occurring and genetically modified murine neurologic mutations; including pages on double knockout animals. Interactive maps of each murine chromosome and human syntenic maps. | epinephrine, gaba, acetylcholine, agonist, antagonist, aspartate, dopamine, glutamate, glycine, human, molecular biology, murine chromosome, mutant, neural, neural factor, neurokine, neurological, neurotransmitter, n eurotrophin, norepinephrine, serotonin, molecular neuroanatomy resource, nervous system, adult, murine | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-11000 | SCR_001143 | 2026-09-03 04:44:19 | 0 | |||||||||
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Phoenix Pharmaceuticals Resource Report Resource Website 1000+ mentions |
Phoenix Pharmaceuticals (RRID:SCR_001141) | commercial organization | Commercial antibody supplier that specializes in peptide-related products for research in obesity, cardiovascular disease, and diabetes. | antibody, peptide, obesity, cardiovascular, diabetes, commercial, biomaterial supply resource | nlx_152429 | SCR_001141 | Phoenix Pharmaceuticals Inc. | 2026-09-03 04:44:24 | 1136 | ||||||||||
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Translational Research Laboratory Resource Report Resource Website |
Translational Research Laboratory (RRID:SCR_001023) | data or information resource, portal, topical portal | Cancer research laboratory at the Peter MacCallum Cancer Centre which investigates biomarkers identification, compounds for activity as anti-cancer drugs, and small molecule targeted therapies. | translational research, cancer, therapeutics, biomarker, small molecule |
is listed by: ScienceExchange is related to: Peter Mac Translational Research Laboratory |
SciEx_10351 | https://www.scienceexchange.com/labs/translational-research-laboratory | http://www.scienceexchange.com/facilities/peter-maccallum-cancer-centre | SCR_001023 | Peter MacCallum Cancer Centre - Cancer Therapeutics Program | 2026-09-03 04:44:17 | 0 | |||||||
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Reaper - Demultiplexing trimming and filtering sequencing data Resource Report Resource Website 1+ mentions |
Reaper - Demultiplexing trimming and filtering sequencing data (RRID:SCR_001144) | Reaper | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. Software program for demultiplexing, trimming and filtering short read sequencing data. | c, alignment, sequence, demultiplex, trim, filter, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:reaper, OMICS_02157 | https://bio.tools/reaper | SCR_001144 | 2026-09-03 04:44:15 | 1 | |||||||
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Phred Resource Report Resource Website 10+ mentions |
Phred (RRID:SCR_001017) | Phred | data analysis software, data processing software, sequence analysis software, software application, software resource | A base calling program for DNA sequence traces. | base calling, sequence analysis software, dna, trace | is listed by: OMICtools | PMID:9521922 | Restricted | OMICS_01809 | SCR_001017 | 2026-09-03 04:44:11 | 13 | |||||||
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Skylign Resource Report Resource Website 10+ mentions |
Skylign (RRID:SCR_001176) | Skylign | analysis service resource, data analysis service, production service resource, service resource, software resource | A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. | sequence alignment, profile, logo, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Janelia Research |
PMID:24410852 | Creative Commons Attribution License, v3 Unported | biotools:skylign, OMICS_02182 | https://bio.tools/skylign | SCR_001176 | Skylign - Interactive logos for alignments and profile HMMs | 2026-09-03 04:44:22 | 13 | |||||
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yaqcaffy Resource Report Resource Website 1+ mentions |
yaqcaffy (RRID:SCR_001295) | yaqcaffy | software resource | Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets. | microarray, one channel, quality control, report writing, affymetrix, gene expression, 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 | BioTools:yaqcaffy, biotools:yaqcaffy, OMICS_02040 | http://www.bioconductor.org/packages/release/bioc/html/yaqcaffy.html | SCR_001295 | yaqcaffy - Affymetrix expression data quality control and reproducibility analysis | 2026-09-03 04:44:28 | 3 | ||||||
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BSSim Resource Report Resource Website 1+ mentions |
BSSim (RRID:SCR_001212) | BSSim | software resource | Software to mimic various methylation level and bisulfite conversion rate in CpG, CHG and CHH context, respectively. It can also simulate genetic variations that are divergent from the reference sequence along with the sequencing error and quality distributions. In the output, both directional/non-directional, various read length, single/paired-end reads and alignment data in the SAM format can be generated. BSSim is a cross-platform BS-seq simulator offers output read datasets not only suitable for Illumina's Solexa, but also for Roche's 454 and Applied Biosystems' SOLiD. | bisulfite sequencing, simulator, next-generation sequencing, python, dna methylation, snp, read quality | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02130 | SCR_001212 | BSSim: Bisulfite sequencing simulator for next-generation sequencing | 2026-09-03 04:44:22 | 1 | |||||||
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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 | SplicePlot: a tool for visualizing alternative splicing | 2026-09-03 04:44:18 | 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 | ChIPsim - Simulation of ChIP-seq experiments | 2026-09-03 04:44:30 | 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 | methyAnalysis - DNA methylation data analysis and visualization | 2026-09-03 04:44:30 | 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 | 2026-09-03 04:44:21 | 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 | les package: Identifying Differential Effects in Tiling Microarray Data, Loci of Enhanced Significance | 2026-09-03 04:44:28 | 0 |
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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."
