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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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umis Resource Report Resource Website 1+ mentions |
umis (RRID:SCR_024381) | software toolkit, software resource | Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias. | estimating expression in RNA-Seq data, sequencing of end tags of transcript, incorporate molecular tags, correct for amplification bias, | is listed by: Debian | PMID:28263961 | Free, Available for download, Freely available, | OMICS_12783 | https://sources.debian.org/src/umis/ | SCR_024381 | 2026-08-09 09:08:53 | 3 | |||||||
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survivalROC Resource Report Resource Website 10+ mentions |
survivalROC (RRID:SCR_024415) | software toolkit, software resource | Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data. | compute time dependent Receiver Operating Characteristic curve, censored survival data, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024415 | survival Receiver Operating Characteristic | 2026-08-09 09:08:28 | 23 | |||||||||
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sra-toolkit Resource Report Resource Website 100+ mentions |
sra-toolkit (RRID:SCR_024350) | software toolkit, software resource | Software collection of tools and libraries for using data in the INSDC Sequence Read Archives.Used for long term storage of the next-generation sequence traces. | using data in the INSDC Sequence Read Archives, long term storage of the next-generation sequence traces, | is listed by: Debian | PMID:19906712 | Free, Available for download, Freely available, | OMICS_03771 | https://sources.debian.org/src/sra-toolkit/ | SCR_024350 | NCBI SRA Toolkit | 2026-08-09 09:08:27 | 271 | ||||||
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MMV Im2Im Resource Report Resource Website 1+ mentions |
MMV Im2Im (RRID:SCR_024630) | software toolkit, software resource | Software Python package for image to image transformation in bioimaging applications. Can be used for semantic segmentation, instance segmentation, image restoration, image generation, and more. | image to image transformation, semantic segmentation, instance segmentation, image restoration, image generation, | DOI:10.48550/arXiv.2209.02498 | Free, Available for download, Freely available | SCR_024630 | MMV_Im2Im | 2026-08-09 09:08:30 | 1 | |||||||||
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ggridges Resource Report Resource Website 1+ mentions |
ggridges (RRID:SCR_024511) | software toolkit, software resource | Software R package enables creation of Ridgeline plots in 'ggplot2' | creation of Ridgeline plots in 'ggplot2', | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/wilkelab/ggridges | SCR_024511 | 2026-08-09 09:09:04 | 8 | |||||||||
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gamm4 Resource Report Resource Website 1+ mentions |
gamm4 (RRID:SCR_024507) | software toolkit, software resource | Software R package to estimate generalized additive mixed models. | estimate generalized additive mixed models, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024507 | 2026-08-09 09:08:29 | 4 | ||||||||||
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Optimization Toolbox Resource Report Resource Website 1+ mentions |
Optimization Toolbox (RRID:SCR_024486) | software toolkit, software resource | Software package provides functions for finding parameters that minimize or maximize objectives while satisfying constraints. Toolbox includes solvers for linear programming, mixed integer linear programming, quadratic programming, second order cone programming, nonlinear programming, constrained linear least squares, nonlinear least squares, nonlinear equations. | Mathworks, finding parameters, minimize or maximize objectives, linear programming solver, mixed integer linear programming solver, quadratic programming solver, second order cone programming solver, nonlinear programming solver, constrained linear least squares solver, nonlinear least squares solver, nonlinear equations solver, | is listed by: SoftCite | Restricted | SCR_024486 | 2026-08-09 09:09:04 | 1 | ||||||||||
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Lightning Pose Resource Report Resource Website |
Lightning Pose (RRID:SCR_024480) | software toolkit, software resource | Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools. | OpenBehavior, animal pose estimation algorithm, Bayesian post processing approach, direct video manipulation, | is listed by: OpenBehavior | Gatsby Charitable Foundation ; NINDS K99NS128075; Irma T Hirschl Trust ; NINDS NS075023; NINDS U19NS123716; NSF ; Simons Foundation |
PMID:37162966 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/lightningpose/ | SCR_024480 | 2026-08-09 09:09:04 | 0 | |||||||
|
CopyKAT Resource Report Resource Website 50+ mentions |
CopyKAT (RRID:SCR_024512) | software toolkit, software resource | Software R package to estimate genomic copy number profiles at average genomic resolution of 5 Mb from read depth in high throughput single cell RNA sequencing data.Used for inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data. | Inference of genomic copy number and subclonal structure of human tumors, high throughput single cell RNAseq data, | is listed by: SoftCite | PMID:33462507 | Free, Available for download, Freely available | SCR_024512 | , Copynumber Karyotyping of Aneuploid Tumors | 2026-08-09 09:08:56 | 84 | ||||||||
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classInt Resource Report Resource Website 1+ mentions |
classInt (RRID:SCR_024515) | software toolkit, software resource | Software R package for choosing univariate class intervals for mapping or other graphics purposes. | choosing univariate class intervals, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/r-spatial/classInt/ | SCR_024515 | Class Intervals | 2026-08-09 09:08:56 | 2 | ||||||||
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mitml Resource Report Resource Website 1+ mentions |
mitml (RRID:SCR_024516) | software toolkit, software resource | Software R package for multiple imputation of missing data in multilevel modeling. | multiple imputation of missing data in multilevel modeling, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/simongrund1/mitml | SCR_024516 | 2026-08-09 09:08:29 | 1 | |||||||||
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OBIWarehouse Resource Report Resource Website |
OBIWarehouse (RRID:SCR_010729) | OBIW | data or information resource, topical portal, portal | OBIWarehouse (Open Biological Warehouse) aims at integrating several biological data sources into a unified database. Content includes 3D structural data, Protein-related data, Metabolic-related data, Genomic-related data, and Biological classification. | has parent organization: PrabiG | nlx_93231 | SCR_010729 | Open Biological Warehouse | 2026-08-10 09:34:04 | 0 | |||||||||
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dictyBase - Teaching Tools Using Dictyostelium discoideum Resource Report Resource Website 1+ mentions |
dictyBase - Teaching Tools Using Dictyostelium discoideum (RRID:SCR_010701) | data or information resource, training material, narrative resource | Dictyostelium discoideum is a great organism to use to teach cellular biology. It exhibits very interesting behaviors, such as chemotaxis and phagocytosis, that can readily be studied in standard laboratories without the need for expensive equipment. Lists of labs being used in real courses settings and all necessary information for performing those experiments are provided. Major headings: * Dictyostelium cell biology course, by Dr. David Knecht, University of Connecticut * Dictyostelium cell biology, by Dr. Derrick Brazill, Hunter College, New York * Report on the number of cells in a slug, contributed by John Bonner * Practical on chemotaxis, by Dr. Thierry Soldati, University of Geneva * Comments from Researchers * References suggested by contributors | has parent organization: Dictyostelium discoideum genome database | nlx_83913 | SCR_010701 | Teaching Tools Using Dictyostelium discoideum | 2026-08-10 09:34:04 | 5 | ||||||||||
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HHpred Resource Report Resource Website 1000+ mentions |
HHpred (RRID:SCR_010276) | data or information resource, database, software resource | The primary aim in developing HHpred was to provide biologists with a method for sequence database searching and structure prediction that is as easy to use as BLAST or PSI-BLAST and that is at the same time much more sensitive in finding remote homologs. In fact, HHpred''s sensitivity is competitive with the most powerful servers for structure prediction currently available. HHpred is the first server that is based on the pairwise comparison of profile hidden Markov models (HMMs). Whereas most conventional sequence search methods search sequence databases such as UniProt or the NR, HHpred searches alignment databases, like Pfam or SMART. This greatly simplifies the list of hits to a number of sequence families instead of a clutter of single sequences. All major publicly available profile and alignment databases are available through HHpred. | nlx_156935 | SCR_010276 | Homology detection & structure prediction by HMM-HMM comparison | 2026-08-10 09:33:59 | 1032 | |||||||||||
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Boyce Thompson Institute for Plant Research Resource Report Resource Website |
Boyce Thompson Institute for Plant Research (RRID:SCR_010716) | BTI | data or information resource, topical portal, portal | BTI is unique in being a private, not-for-profit research institute dedicated to plant biology, and located on a major university campus. Its mission is to advance and communicate scientific knowledge in plant biology to improve agriculture, protect the environment, and enhance human health. The institute was founded in Yonkers, New York, next to the home of its benefactor, William Boyce Thompson. In the mid-1970''s, however, it was recognized that a physical presence on a university campus would catapult the institute to a higher level of research, and the Cornell affiliation was born. BTI hires its own faculty, postdoctoral scholars and technicians, but also hosts undergraduate and graduate researchers from Cornell. BTI faculty generally have adjunct appointments at Cornell, and participate in graduate training and other university affairs. As envisioned in the Agreement of Affiliation, the partnership is advantageous for both parties, and contributes to a singularly strong environment for fundamental plant research on the campus. William Boyce Thompson founded BTI in 1924 on the premise that basic plant research leads to real benefits for people. Many potential applications of BTI research are to improve crops by increasing yield or nutritional content, or decreasing the need for harmful fertilizers and pesticides. Other research could lead to inexpensive plant-made vaccines, or even shed light on the human immune system. With aims like these in mind, scientists at BTI study life at the scale of genes and proteins to learn about processes such as how plants detect light, or how they respond when aphids bite into them. Along with research, BTI''s mission includes environmental responsibility and outreach to teachers, students, and community members. Though it remains an independent, non-profit institution, BTI is affiliated with Cornell University and is located on its Ithaca, New York campus. |
has parent organization: Cornell University; New York; USA is parent organization of: SGN is parent organization of: Sol Genomics Network - Bulk download |
nlx_89613 | SCR_010716 | Boyce Thompson Institute | 2026-08-10 09:34:04 | 0 | |||||||||
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fanDTasia Java Applet: DT-MRI Processing Resource Report Resource Website 1+ mentions |
fanDTasia Java Applet: DT-MRI Processing (RRID:SCR_009624) | fdt | software application, data processing software, image processing software, software resource | A Java applet tool for DT-MRI processing. It opens Diffusion-Weighted MRI datasets from user's computer and performs very efficient tensor field estimation using parallel threaded processing on user's browser. No installation is required. It runs on any operating system that supports Java (Windows, Mac, Linux,...). The estimated tensor field is guaranteed to be positive definite second order or higher order and is saved in user's local disc. MATLAB functions are also provided to open the tensor fields for your convenience in case you need to perform further processing. The fanDTasia Java applet provides also vector field visualization for 2nd and 4th-order tensors, as well as calculation of various anisotropic maps. Another useful feature is 3D fiber tracking (DTI-based) which is also shown using 3d graphics on the user's browser. | magnetic resonance, dti, diffusion-weighted mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Florida; Florida; USA |
NIBIB EB007082; NINDS NS066340 |
Non-Commercial Software License Agreement, Https://www.nitrc.org/include/glossary.php#589, Non-commercial | nlx_155849 | http://www.nitrc.org/projects/fandtasia | SCR_009624 | FanDTasia | 2026-08-10 09:33:45 | 2 | |||||
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Down Syndrome Center for Research and Treatment Resource Report Resource Website |
Down Syndrome Center for Research and Treatment (RRID:SCR_010627) | DSCRT | data or information resource, topical portal, portal | The Down Syndrome Center for Research and Treatment (DSCRT) is one of the first programs in the country to connect academic research with treatment of adults and children with Down syndrome. Our goal is to apply cutting edge basic research to develop treatments that will help people with Down syndrome improve their cognition and forestall the onset of Alzheimer''s disease. Members of this special population continue to live fuller, healthier lives. We hope to build on this progress and advance their potential even further. About 400,000 people with Down syndrome live in the U.S. today, and one in every 733 babies is born with the condition. Children with Down syndrome are at risk for congenital heart defects, respiratory and hearing problems, childhood leukemia, and thyroid conditions. They typically also have mild to moderate cognitive impairment that affects learning, memory and speech. This is an important topic for research. With increased health care, education, and societal support, people with Down syndrome are living longer, fuller lives. But as they age we are discovering an increased occurrence of the symptoms associated with Alzheimer''s disease. In fact, about 25 percent of individuals with Down syndrome over age 35 increasingly show clinical signs and symptoms of Alzheimer''s type dementia. By age 60, more than half show cognitive decline. | has parent organization: University of California San Diego School of Medicine; California; USA | Aging | nlx_58054 | SCR_010627 | 2026-08-10 09:34:03 | 0 | |||||||||
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Molecular Biology Gateway Resource Report Resource Website |
Molecular Biology Gateway (RRID:SCR_010628) | data or information resource, topical portal, portal | Molecular Biology Gateway is the gateway to Web resources for molecular biology, genomics, PCR, protocols, microbiology, and biochemistry. Major categories include: Current Molecular Biology News, Microbiology, Virology, Genomics and Bioinformatics, PCR, Journals, Books, and other Publications, Protocols, Technology, Books, and Recommended Reading. | nlx_59283 | SCR_010628 | 2026-08-10 09:34:03 | 0 | ||||||||||||
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Integrated Datasets Resource Report Resource Website |
Integrated Datasets (RRID:SCR_010503) | data or information resource, database, catalog | A virtual database cataloging numerous data set resources, including: BrainMaps.org, Cell Centered Database, Clinical Trials Network (CTN) Data Share, ClinicalTrials.gov, CRCNS, Gene Expression Omnibus, ArrayExpress, MPD - Mouse Phenome Database, BioSharing, Gene Weaver, XNAT Central, 1000 Functional Connectomes Project, Health.Data.gov, SciCrunch Registry, NIF Registry Automated Crawl Data, NeuroVault, OpenfMRI, Physiobank, RanchoBiosciences, YPED, Data.gov Science, and Research Data Catalog. | data set, database, integrated, catalog, data set resource |
uses: BrainMaps.org uses: Cell Centered Database uses: NIDA Data Share uses: ClinicalTrials.gov uses: CRCNS uses: Gene Expression Omnibus uses: ArrayExpress uses: Mouse Phenome Database (MPD) uses: FAIRsharing uses: Gene Weaver uses: XNAT Central uses: 1000 Functional Connectomes Project uses: Health.Data.gov uses: SciCrunch Registry uses: NIF Registry Automated Crawl Data uses: NeuroVault uses: OpenNeuro uses: Physiobank uses: RanchoBiosciences uses: YPED uses: Data.gov Science and Research Data Catalog is used by: NIF Data Federation has parent organization: Omics Discovery Index has parent organization: Integrated has parent organization: SciCrunch |
Data are licensed by their respective owners. Use and distribution is subject to the Terms of Use by the original resource as well as the, Creative Commons Attribution License | nlx_158508 | https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-18 | SCR_010503 | Integrated Data sets, Integrated Catalog of Datasets | 2026-08-10 09:34:00 | 0 | |||||||
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Annmap Resource Report Resource Website 1+ mentions |
Annmap (RRID:SCR_011783) | Annmap | data or information resource, database, software resource | A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser. | is listed by: OMICtools | Cancer Research UK ; Cancer Research UK Manchester Institute |
OMICS_00900 | SCR_011783 | 2026-08-10 09:34:20 | 6 |
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