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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GapMis Resource Report Resource Website |
GapMis (RRID:SCR_001999) | software resource | A software tool for pairwise sequence alignment with a single gap. | standalone software | is listed by: OMICtools | PMID:22974258 | Free, Available for download, Freely available | OMICS_03692 | SCR_001999 | 2026-07-25 12:05:14 | 0 | ||||||||
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TRAMS Resource Report Resource Website 1+ mentions |
TRAMS (RRID:SCR_002003) | TRAMS | software resource | A software program for functional annotation of genomic single nucleotide polymorphisms (SNPs) which is available to download as a single file executable for WINDOWS users with limited computational experience and as a Python script for Mac OS and Linux users. It needs only a tab delimited text file containing SNP locations, reference nucleotide and SNPs in different strains along with a reference genome sequence in standard GenBank or EMBL format. It annotates SNPs as synonymous, non-synonymous or nonsense. Non-synonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms (MNPs) within a codon are combined prior to annotation. A workflow has also been developed for use in Galaxy to map short reads to a reference genome and extract and annotate the SNPs. | single nucleotide polymorphism, windows, python, mac os, linux, synonymous, non-synonymous, nonsense, annotate, genomic variation |
is listed by: OMICtools is related to: Galaxy has parent organization: FigShare |
PMID:23828175 | Free, Available for download, Freely available | OMICS_01924 | SCR_002003 | Tool for Rapid Annotation of Microbial SNPs, Tool for rapid annotation of microbial SNPs: a simple program for rapid annotation of genomic variation in prokaryotes, Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes, TRAMS: a simple program for rapid annotation of genomic variation in prokaryotes | 2026-07-25 12:05:18 | 1 | ||||||
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Vennt Resource Report Resource Website 1+ mentions |
Vennt (RRID:SCR_002083) | software resource | A web-tool to generate dynamic Venn diagrams for differential gene expression. | unix/linux, mac os x, windows, python | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_03549 | https://github.com/drpowell/vennt | SCR_002083 | Vennt - Dynamic Venn diagrams for Differential Gene Expression | 2026-07-25 12:05:16 | 7 | |||||||
|
TEQC Resource Report Resource Website 10+ mentions |
TEQC (RRID:SCR_001943) | software resource | An R/Bioconductor package for quality assessment of target enrichment experiments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on. | standalone software, unix/linux, mac os x, windows, r, genetics, microarray, quality control, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21398674 | Free, Available for download, Freely available | OMICS_03602 | SCR_001943 | TEQC - Quality control for target capture experiments | 2026-07-25 12:05:13 | 14 | |||||||
|
flowViz Resource Report Resource Website 10+ mentions |
flowViz (RRID:SCR_002075) | software resource | Software that provides visualization tools for flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18245128 | Free, Available for download, Freely available | OMICS_05615 | SCR_002075 | flowViz - Visualization for flow cytometry | 2026-07-25 12:05:16 | 30 | |||||||
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PyroBayes Resource Report Resource Website 1+ mentions |
PyroBayes (RRID:SCR_003757) | PyroBayes | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A base caller for pyrosequences from the 454 Life Sciences sequencing machines. | is listed by: OMICtools | PMID:18193056 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01155 | SCR_003757 | 2026-07-25 12:05:42 | 3 | ||||||||
|
Oxford Nanopore Technologies Resource Report Resource Website 100+ mentions |
Oxford Nanopore Technologies (RRID:SCR_003756) | Oxford Nanopore | commercial organization | Commercial organization developing a disruptive, proprietary technology platform for the direct, electronic analysis of single molecules. The instruments GridION and MinION are adaptable for the analysis of DNA, RNA, proteins, small molecules and other types of molecule. Consequently, the platform has a broad range of potential applications, including scientific research, personalized medicine, crop science and security / defence. | nanopore technology, dna, rna, protein, small molecule, molecule, analysis, nanopore, nanopore sensing |
is related to: READNA is related to: Pychopper |
nlx_158233 | SCR_003756 | Oxford Nanopore Technologies Ltd | 2026-07-25 12:05:43 | 399 | ||||||||
|
Brandeis University; Massachusetts; USA Resource Report Resource Website |
Brandeis University; Massachusetts; USA (RRID:SCR_003669) | university | Private research university located in the Boston suburb of Waltham, Massachusetts. Founded in 1948 as a non-sectarian, coeducational institution sponsored by the Jewish community, Brandeis was established on the site of the former Middlesex University. |
is parent organization of: Paper Rejection Repository is parent organization of: Enhancer Trap Line Browser is parent organization of: Brandeis University Neuroscience Undergraduate Program is parent organization of: Brandeis University Neuroscience Graduate Program is parent organization of: Research Network in Early Experience and Brain Development is parent organization of: Neurofitter is parent organization of: Brandeis University Light Microscopy Core Facility is parent organization of: Brandeis University Louise Mashal Gabbay Cellular Visualization Center Electron Microscopy Core Facility |
nlx_50198, Wikidata:Q49119, ISNI:0000 0004 1936 9473, grid.253264.4, Crossref funder ID:100007864 | https://ror.org/05abbep66 | SCR_003669 | 2026-07-25 12:05:41 | 0 | ||||||||||
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eBioscience Resource Report Resource Website 50+ mentions |
eBioscience (RRID:SCR_003660) | commercial organization | An Antibody supplier | nlx_152349 | SCR_003660 | 2026-07-25 12:05:43 | 70 | ||||||||||||
|
Signalway Resource Report Resource Website 10+ mentions |
Signalway (RRID:SCR_003659) | SAB | commercial organization | An Antibody supplier | nlx_152462 | SCR_003659 | Signalway Antibody Co. Ltd | 2026-07-25 12:05:41 | 11 | ||||||||||
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RAREMETAL Resource Report Resource Website 10+ mentions |
RAREMETAL (RRID:SCR_003573) | RAREMETAL | software resource | A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan; Ann Arbor; USA |
PMID:24894501 | biotools:raremetal, OMICS_00243 | https://bio.tools/raremetal | SCR_003573 | 2026-07-25 12:05:41 | 22 | |||||||
|
Corpus Callosum Thickness Profile Analysis Pipeline Resource Report Resource Website |
Corpus Callosum Thickness Profile Analysis Pipeline (RRID:SCR_003575) | ccsegthickness | software resource | An end-to-end pipeline for corpus callosum processing that provides automated midsagittal alignment, CC segmentation with a quality control tool, and thickness profile generation. Groupwise analysis is facilitated by permutation testing with FWER and FDR multiple comparison correction. Results display is facilitated by a display script that shows p-values on a 3D pipe representation of a CC. This pipeline is implemented in MATLAB and requires the Image Processing Toolbox. There are plans to implement it completely in Python. | linux, matlab, mr, nifti-1, posix/unix-like, corpus callosum | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:24968872 | GNU General Public License | nlx_157716 | SCR_003575 | 2026-07-25 12:05:40 | 0 | |||||||
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Myelin Repair Foundation Resource Report Resource Website 1+ mentions |
Myelin Repair Foundation (RRID:SCR_003723) | MRF | institution | A non-profit foundation that funds basic research and is focused on accelerating the development of myelin repair therapeutics for multiple sclerosis. They have defined a 15-year research plan to develop a drug or drugs and believes its Accelerated Research Collaborative (ARC) model can subsequently be used to accelerate the treatment for all diseases. The ARC framework coordinates and manages the entire therapeutic development continuum from discovery biology to FDA approval. The model works by coordinating multi-disciplinary basic research from academic and government laboratories, systematically validating and derisking potential compounds/targets, and collaborating with pharma partners to increase the probability of successful programs. | consortium, drug, myelin repair, therapeutic, myelin, drug development | is listed by: Consortia-pedia | Multiple Sclerosis, Neurological disease | nlx_157901, grid.429475.9, Wikidata: Q6947290 | https://ror.org/05yb6xa82 | SCR_003723 | 2026-07-25 12:05:43 | 3 | |||||||
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Tocris Bioscience Resource Report Resource Website 100+ mentions |
Tocris Bioscience (RRID:SCR_003689) | commercial organization | An Antibody supplier | nlx_152479 | SCR_003689 | 2026-07-25 12:05:42 | 387 | ||||||||||||
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TransCelerate BioPharma Resource Report Resource Website 1+ mentions |
TransCelerate BioPharma (RRID:SCR_003728) | TransCelerate | nonprofit organization | Non-profit research organization aiming to accelerate drug development by increasing the quality and efficiency of clinical studies through the development of shared tools, methods, and platforms. Consortium partnerships are limited to pharmaceutical and biotechnology companies with research & development operations, although there are collaborations with external organizations such the Clinical Data Interchange Standards Consortium (CDISC). Its current focus is to collaborate on: * Standardizing risk-based monitoring * Development of methods to qualify and train clinical trial sites * Development of a common investigator web portal * Development of clinical data standards on efficacy, and methods for comparator drug trials It currently has 5 projects: # Standardized Approach for High-Quality, Risk-Based Monitoring program aims to develop an industry-wide standard and approach for risk-based monitoring of clinical trials in order to enhance patient safety and ensure the quality of clinical trial data. # Shared Site Qualification and Training program aims to standardize GCP training and site qualification credentials in order to realize efficiencies and accelerate study start-up timelines. # Common Investigator Site Portal is a platform designed to streamline investigator and site access through harmonized delivery of content and services. # Data Standards project is a partnership with CDISC to develop industry-wide data standards in priority therapeutic areas to support the exchange and submission of clinical research and meta-data, improving patient safety and outcomes. # Comparator Drugs project aims to establish reliable, rapid sourcing of quality products for use in clinical trials through a comparator supply model enabling accelerated trial timelines and enhanced patient safety. | drug, clinical trial, multipharma, data sharing, drug development, consortium, medicine, clinical, standard specification | is listed by: Consortia-pedia | Member companies financial contributions ; Member companies in-kind contributions ; GlaxoSmithKline |
nlx_157913 | SCR_003728 | TransCelerate BioPharma Inc. | 2026-07-25 12:05:42 | 4 | |||||||
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Philips Research Resource Report Resource Website |
Philips Research (RRID:SCR_003871) | commercial organization | A global organization that helps Philips introduce innovations that improve people's lives by providing technology options for innovations in the area of health and well-being, targeted at both developed and emerging markets. Positioned at the front-end of the innovation process, they work on everything from spotting trends and ideation to proof of concept and - where needed - first-of-a-kind product development. | health, well-being, technology |
is related to: READNA has parent organization: Philips |
nlx_158235 | SCR_003871 | 2026-07-25 12:05:45 | 0 | ||||||||||
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Roslin Cells Resource Report Resource Website 1+ mentions |
Roslin Cells (RRID:SCR_003857) | Roslin Cells | commercial organization | Organization that supplies undifferentiated, clinical grade, human pluripotent stem cell lines to the life science community, and works with academic, clinical and commercial colleagues to enable and facilitate the use of these high grade cells in the development of new reagents, drugs and cellular therapeutics. They also seek to drive the economic development of the stem cell sector in Scotland. Their products can act as a valuable tool in supporting clients' drug discovery, development and clinical research programmes. | pluripotent stem cell, induced pluripotent stem cell, cell therapy, embryonic stem cell line, clinical grade |
is listed by: One Mind Biospecimen Bank Listing is parent organization of: EBiSC |
nlx_158181 | SCR_003857 | Roslin Cells Ltd | 2026-07-25 12:05:43 | 2 | ||||||||
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PEAR Resource Report Resource Website 500+ mentions |
PEAR (RRID:SCR_003776) | PEAR | software resource | Software for an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. | next-generation sequencing, sequence analysis |
is listed by: OMICtools has parent organization: Heidelberg Institute for Theoretical Studies; Heidelberg; Germany |
PMID:24142950 | OMICS_00674 | SCR_003776 | Pair-end read merger, PEAR: Pair-end read merger | 2026-07-25 12:05:42 | 854 | |||||||
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Electro Scientific Industries Resource Report Resource Website |
Electro Scientific Industries (RRID:SCR_003895) | ESI | commercial organization | A high technology company that is a developer and supplier of photonic and laser systems for microelectronics manufacturers. They manufacture a variety of products for testing and repairing equipment, and particularly products designed for use by manufacturers of other high-tech products. These include laser trimming systems. (Adapted from Wikipedia) | microengineering, electronics, semiconductor, testing, repair, laser trimming system, photonic, laser, microelectronics | is related to: ONE Study | nlx_158228 | SCR_003895 | Electro Scientific Industries Inc. | 2026-07-25 12:05:44 | 0 | ||||||||
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Inserm Transfert Resource Report Resource Website |
Inserm Transfert (RRID:SCR_003808) | commercial organization | A private subsidiary of the French National Institute of the Health and Medical Research (Inserm), dedicated to technology transfer (from invention disclosure to industrial partnership). It manages European and International research projects, supports large scale projects in epidemiology and public health. It has run a proof of concept fund. The company is also committed to seed financing in the biotech sector, through its dedicated seed fund company Inserm Transfert Initiative. www.inserm-transfert.fr | technology transfer, epidemiology, public health |
is related to: AgedBrainSYSBIO has parent organization: National Institute of Health and Medical Research; Rennes; France is parent organization of: AgedBrainSYSBIO |
nlx_158128, grid.14498.30 | https://ror.org/01wftfc57 | SCR_003808 | Inserm-Transfert SA, Inserm Transfert SA | 2026-07-25 12:05:44 | 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."
