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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GUARDD Resource Report Resource Website |
GUARDD (RRID:SCR_000040) | software resource | MATLAB software designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD NMR data. | standalone software, matlab, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:22160811 | Free, Available for download, Freely available | biotools:guardd, OMICS_04020 | https://bio.tools/guardd | SCR_000040 | SciCrunch Registry | Graphical User-friendly Analysis of Relaxation Dispersion Data | 2026-10-31 12:12:32 | 0 | ||||||
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flowCL Resource Report Resource Website |
flowCL (RRID:SCR_000046) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations. | software package, mac os x, unix/linux, windows, r, flow cytometry |
has parent organization: Bioconductor has parent organization: BC Cancer Agency |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05594 | SCR_000046 | SciCrunch Registry | flowCL - Semantic labelling of flow cytometric cell populations | 2026-10-31 12:12:33 | 0 | ||||||||
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CG-Pipeline Resource Report Resource Website |
CG-Pipeline (RRID:SCR_000047) | software resource | A software tool for assembling genome sequence data and running feature prediction and annotation tools on the assembly. | perl | has parent organization: SourceForge | PMID:20519285 | Free, Available for download, Freely available | OMICS_04062 | http://sourceforge.net/projects/cg-pipeline/ | SCR_000047 | SciCrunch Registry | 2026-10-31 12:12:32 | 0 | |||||||
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Cbrowse Resource Report Resource Website |
Cbrowse (RRID:SCR_000044) | software resource | Software providing an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. | unix/linux, mac os x, windows |
has parent organization: Google Code has parent organization: Miami University; Ohio; USA |
PMID:22789590 | Free, Available for download, Freely available | OMICS_04048 | SCR_000044 | SciCrunch Registry | 2026-10-31 12:12:32 | 0 | ||||||||
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Institute for Magnetic Resonance Safety, Education and Research Resource Report Resource Website 1+ mentions |
Institute for Magnetic Resonance Safety, Education and Research (RRID:SCR_000039) | institution | The Institute for Magnetic Resonance Safety, Education, and Research (IMRSER) was formed in response to the growing need for information and research on matters pertaining to magnetic resonance (MR) safety. The IMRSER is the first independent, multidisciplinary, professional organization devoted to promoting awareness, understanding, and communication of MR safety issues through education and research. Mission Statement To promote awareness and understanding of MR safety, To disseminate information regarding current and emerging MR safety issues, To develop and provide materials and resources to facilitate MR safety-related education and training, To respond to critical MR safety issues with a sense of urgency, and To advance the field of MR safety through support of scientific research. Functions and activities of the IMRSER include development of up-to-date MR safety materials and dissemination of this information to the MR community. This is accomplished predominantly through the efforts of the Advisory Boards. Members of the Advisory Boards of the Institute for Magnetic Resonance Safety, Education, and Research (IMRSER) are charged with creating recommendations, guidelines, position papers, and educational materials pertaining to existing or emerging MR safety issues. This is achieved by utilizing the pertinent peer-reviewed literature and by relying on each members extensive clinical, research, or other appropriate experience. Notably, documents developed by the IMRSER incorporate MR safety guidelines and recommendations created by the International Society for Magnetic Resonance in Medicine (ISMRM), the American College of Radiology (ACR), the Food and Drug Administration (FDA), the National Electrical Manufacturers Association (NEMA), the Medical Devices Agency (MDA), the International Electrotechnical Commission (IEC), and other similar organizations. The IMRSERs rigorous development and review process for MR safety documents ensures that authoritative and relevant information is produced in a timely manner for rapid dissemination to the MR community. The MR safety information is provided to MR healthcare professionals and others as hard copy and electronic publications. Additionally, this information is posted on the IMRSER web site as well as on www.MRIsafety.com (currently with over 92,000 registered users). The Institute for Magnetic Resonance Safety, Education, and Research permits all members of the MR community to use the MRI Safety Guidelines posted on this web site. Please be sure to read and understand our disclaimer. | guidelines, human, magnetic resonance, mri, safety | nif-0000-10678 | SCR_000039 | SciCrunch Registry | IMRSER | 2026-10-31 12:12:32 | 1 | ||||||||||
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TADS - Treatment for Adolescents with Depression Study Resource Report Resource Website 1+ mentions |
TADS - Treatment for Adolescents with Depression Study (RRID:SCR_000037) | TADS | clinical trial, data or information resource, disease-related portal, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Multi-site clinical research study examining the short- and long-term effectiveness of an antidepressant medication and psychotherapy alone and in combination for treating depression in adolescents ages 12 to 17. For teens treated in TADS, the trial is designed to provide best-practice practical care for depression. | clinical trial, adolescent, major depressive disorder, depressive disorder, cognitive behavioral therapy, psychotherapy, drug, fluoxetine, nct00006286, young human |
is used by: Limited Access Datasets From NIMH Clinical Trials has parent organization: Duke University School of Medicine; North Carolina; USA has parent organization: ClinicalTrials.gov |
Major Depressive Disorder, Depressive Disorder | NIMH 1U01MH064107-01A1 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_146236 | SCR_000037 | SciCrunch Registry | Treatment for Adolescents with Depression Study (TADS), Treatment for Adolescents with Depression Study | 2026-10-31 12:12:32 | 2 | |||||
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University of Tennessee Genome Science and Technology Graduate Program Resource Report Resource Website |
University of Tennessee Genome Science and Technology Graduate Program (RRID:SCR_000038) | UTK GST, UT Knoxville GST | data or information resource, graduate program resource, organization portal, portal | Graduate School of Genome Science and Technology (GST) is a Life Science graduate program founded on two premises. First, whole-genome sequences and related large-scale datasets have transformed how we perform biological research, a trend that is gathering momentum and is anticipated to frame the way the biology research is accomplished for many years to come. Second, advances in technology, whether at the level of instrumentation, computation, or wet lab reagents, have long been a powerful driving force in biology. The GST program is home to faculty mentors from many walks of life. The virulence factors of pathogenic fungi and the engineering of photosynthetic reaction complexes for bioenergy harvesting are just two examples from the cornucopia of research projects being pursued in GST. | genome, molecular genetics, biochemistry, bioinformatics | has parent organization: University of Tennessee Knoxville; Tennessee; USA | nlx_149162 | SCR_000038 | SciCrunch Registry | UTK Genome Science & Technology, UT Genome Science & Technology, UT-ORNL Graduate School of Genome Science and Technology, Graduate School of Genome Science and Technology, University of Tennessee Genome Science & Technology, University of Tennessee Genome Science Technology | 2026-10-31 12:12:32 | 0 | ||||||||
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BlackOPs Resource Report Resource Website |
BlackOPs (RRID:SCR_000032) | data analysis software, data processing software, sequence analysis software, software application, software resource | Open source software tool that simulates experimental RNA-seq and DNA whole exome sequences derived from reference genome, aligns these sequences by custom parameters, detects variants and outputs blacklist of positions and alleles caused by mismapping. Used to characterize mappability of RNA-Seq reads and create blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls. | rna seq, false positive, genome editing, rna editing, mismapped reads | has parent organization: SourceForge | PMID:23935067 | Free, Available for download, Freely available | OMICS_01229 | SCR_000032 | SciCrunch Registry | BlackOPs: RNA-Seq Variant Blacklist Tool | 2026-10-31 12:12:32 | 0 | |||||||
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RCSB PDB Software Tools Resource Report Resource Website 1+ mentions |
RCSB PDB Software Tools (RRID:SCR_000035) | data or information resource, portal, software resource, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Information Portal to Biological Macromolecular Structures provides variety of software tools made available through the RCSB. These tools include: data extraction and deposition preparation tools, data format conversion and validation tools, data parsing tools, dictionary and data management tools, visualization tools that support PDBx/mmCIF, and other PDBx/mmCIF software library tools. | Information Portal, Biological Macromolecular Structure, RCSB, RCSB software tools, data extraction, format conversion, data parsing, data management, visualization, pdbx/mmcif, pdbx, mmcif |
is listed by: LabWorm is related to: Protein Data Bank Markup Language has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31399 | SCR_000035 | SciCrunch Registry | RCSB Software Tools | 2026-10-31 12:12:32 | 2 | ||||||||
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RmiR.Hs.miRNA Resource Report Resource Website |
RmiR.Hs.miRNA (RRID:SCR_000101) | software resource | Software package for various databases of microRNA Targets. | software package, unix/linux, mac os x, windows, r, annotation data, custom db schema, mirna |
is listed by: OMICtools is related to: CRAN has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05797 | SCR_000101 | SciCrunch Registry | RmiR.Hs.miRNA: Various databases of microRNA Targets | 2026-10-31 12:12:33 | 0 | ||||||||
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GeneTex Resource Report Resource Website 500+ mentions |
GeneTex (RRID:SCR_000069) | commercial organization | An antibody supplier for the purposes of life science and biomedical research. This company has a wide variety of immunological reagents that focus on areas of research such as cancer, cell biology, epigenetics, immunology and infectious diseases. | antibody, antibodies, supplier, immunology, research, cell biology, cancer, epigenetics, infectious diseases, reagents | nlx_152372 | SCR_000069 | SciCrunch Registry | 2026-10-31 12:12:33 | 691 | |||||||||||
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nFuse Resource Report Resource Website 1+ mentions |
nFuse (RRID:SCR_000066) | nFuse | software resource | Software that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS). | cancer, genomics |
is listed by: OMICtools is listed by: Google Code has parent organization: Simon Fraser University; British Columbia; Canada |
Cancer | PMID:22745232 | Free, Available for download, Freely available, | OMICS_01353 | SCR_000066 | SciCrunch Registry | nFuse: Discovery of Complex Genomic Rearrangements in Cancer | 2026-10-31 12:12:33 | 2 | |||||
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GASV Resource Report Resource Website 1+ mentions |
GASV (RRID:SCR_000061) | GASV | data analysis software, data processing software, software application, software resource | Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions. | paired-end sequencing data, structural variant, probabilistic algorithm, discordant fragment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GASVPro has parent organization: Brown University; Rhode Island; USA |
ADVANCE Program at Brown University ; Burroughs Wellcome Fund ; Department of Defense Breast Cancer Research ; NSF 0548311 |
PMID:19477992 | Free, Available for download, Freely available | biotools:gasv, OMICS_01352 | http://compbio.cs.brown.edu/projects/gasv/, https://bio.tools/gasv | SCR_000061 | SciCrunch Registry | Geometric Analysis of Structural Variants | 2026-10-31 12:12:33 | 4 | ||||
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ChIPmeta Resource Report Resource Website |
ChIPmeta (RRID:SCR_000054) | data analysis software, data processing software, software application, software resource | Software using a Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets. | chip-chip, chip-seq, ChIP-chip and ChIP-seq datasets analysis, | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02172 | SCR_000054 | SciCrunch Registry | ChIPmeta with HHM | 2026-10-31 12:12:32 | 0 | ||||||||
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FACS Resource Report Resource Website 1+ mentions |
FACS (RRID:SCR_000055) | FACS | software resource | Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence. | unix/linux, sequence, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SciLifeLab |
PMID:20472541 | Free, Available for download, Freely available | OMICS_02147, biotools:facs | https://bio.tools/facs | SCR_000055 | SciCrunch Registry | Fast and Accurate Classification of Sequences | 2026-10-31 12:12:33 | 6 | |||||
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Batman-Seq Resource Report Resource Website |
Batman-Seq (RRID:SCR_000048) | Batman-Seq | software resource | A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment. | c++ | is hosted by: SourceForge | Free, Available for download, Freely available | OMICS_00651 | SCR_000048 | SciCrunch Registry | Basic Alignment Tool for MAny Nucleotides | 2026-10-31 12:12:32 | 0 | |||||||
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University at Buffalo SMBS Department of Pharmacology and Toxicology Resource Report Resource Website |
University at Buffalo SMBS Department of Pharmacology and Toxicology (RRID:SCR_004204) | data or information resource, department portal, organization portal, portal | The Department of Pharmacology and Toxicology strives to maintain excellence in the areas of research, teaching and service to the School, University, and Community. The Department offers a program of didactic course work and research training leading to the degree of Doctor of Philosophy in Pharmacology, either through the Interdisciplinary Graduate Program in Biomedical Sciences (IGPBS) or through the Medical Scientist Training Program (MSTP). Pharmacology and Toxicology have similar basic principles and often utilize similar experimental methods and approaches to address a wide range of biomedical and health-related questions. Both are sciences that are basic not only to medicine, but also to pharmacy, nursing, dentistry, public health, and veterinary medicine. Additional programs are offered for the Bachelor of Science, or a combined Bachelor of Science / Master of Science in Pharmacology and Toxicology, and a Master of Arts in Pharmacology. The graduate programs are structured to provide the candidate with a broad training in basic areas of pharmacology as well as a degree of expertise in one research area including: Neuropharmacology, Psychopharmacology, Toxicology, Molecular and Cellular Pharmacology, Clinical Pharmacology | has parent organization: University at Buffalo School of Medicine and Biomedical Sciences; New York; USA | nif-0000-02077 | SCR_004204 | SciCrunch Registry | UB SMBS Dept. of Pharmacology and Toxicology | 2026-10-31 12:13:44 | 0 | ||||||||||
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Wikikidney.org Resource Report Resource Website |
Wikikidney.org (RRID:SCR_004288) | data or information resource, narrative resource, portal, topical portal, wiki | Wikikidney.org is an effort to prevent kidney diseases and achieve better outcomes in those who have end stage renal disease. Our mission is to use this medium to make the public more aware of kidney disease in a sincere effort to prevent it when we can, and to help our colleagues achieve good outcomes in those who already have end stage renal disease. Our role is to provide as much information as possible to patients, professionals and the general public, with the hopes that this education will be a motivating factor in making the necessary changes to prevent or stall chronic kidney disease. After nearly two decades of seeing patients with end stage renal disease, it is apparent that much of what we deal with can be delayed or prevented altogether. Several medical trials and innovations in the last several years have confirmed these observations, and form the basis of this website. A major element in preventing renal illness is simply early detection, and for this one needs education. As the Internet expands and becomes more and more a tool of everyday life, we will have the ability to access and distribute information like no other generation before us. Qualified readers are encouraged to contribute to existing articles and to create articles of their own. Contents * 1 Kidney Resources - NIC * 2 Especially for Patients * 3 General Kidney Resources * 4 Issues in Nephrology * 5 Clinical Wiki Projects * 6 Be an author, editor or reviewer on wikikidney * 7 Clinical Trials * 8 Newsdesk Top Stories * 9 Essential Physician Resources * 10 Organizations * 11 Government Agencies * 12 Vendor and other Sites * 13 Patents * 14 Index | nlx_30377 | SCR_004288 | SciCrunch Registry | Wikikidney, Wiki.Nephron.org | 2026-10-31 12:13:50 | 0 | |||||||||||
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Echelon Biosciences Resource Report Resource Website 50+ mentions |
Echelon Biosciences (RRID:SCR_004169) | EBI | commercial organization | An Antibody supplier | nlx_152350 | SCR_004169 | SciCrunch Registry | Echelon Biosciences Inc., Echelon Biosciences Incorporated | 2026-10-31 12:13:43 | 76 | ||||||||||
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Brain Architecture Project Resource Report Resource Website 10+ mentions |
Brain Architecture Project (RRID:SCR_004283) | data or information resource, portal, topical portal | Evolving portal that will provide interactive tools and resources to allow researchers, clinicians, and students to discover, analyze, and visualize what is known about the brain's organization, and what the evidence is for that knowledge. This project has a current experimental focus: creating the first brainwide mesoscopic connectivity diagram in the mouse. Related efforts for the human brain currently focus on literature mining and an Online Brain Atlas Reconciliation Tool. The primary goal of the Brain Architecture Project is to assemble available knowledge about the structure of the nervous system, with an ultimate emphasis on the human CNS. Such information is currently scattered in research articles, textbooks, electronic databases and datasets, and even as samples on laboratory shelves. Pooling the knowledge across these heterogeneous materials - even simply getting to know what we know - is a complex challenge that requires an interdisciplinary approach and the contributions and support of the greater community. Their approach can be divided into 4 major thrusts: * Literature Curation and Text Mining * Computational Analysis * Resource Development * Experimental Efforts | central nervous system, connectivity, mapping, model, neuroanatomy, organism, post-mortem, structure, nervous system, structure, human, mouse, brain, zebra finch, addiction gene, addiction |
is used by: BICCN lists: Allen Institute for Brain Science lists: University of California at Los Angeles; California; USA is related to: Mouse Brain Architecture Project is related to: BICCN Anatomy and Morphology Project is related to: Allen Institute for Brain Science has parent organization: Cold Spring Harbor Laboratory is parent organization of: Human Brain Connectivity Database is parent organization of: OBART is parent organization of: Zebrafinch Brain Architecture Project is parent organization of: Mouse Brain Architecture Project |
W. M. Keck Foundation ; NIMH ; NIDA ; Crick-Clay Professorship in Biomathematics at CSHL ; Mathers Foundation ; Simons Foundation |
Free, Public | nlx_143664 | SCR_004283 | SciCrunch Registry | BrainArchitecture.org, BrainArchitecture | 2026-10-31 12:13:45 | 14 |
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