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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SpikeHunter Resource Report Resource Website 1+ mentions |
SpikeHunter (RRID:SCR_024831) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins. | identifying phage tailspike proteins, phage tailspike protein, deplolymerase, right-handed beta-helix, | NLM ; NSF |
PMID:37503040 | Free, Available for download, Freely available | SCR_024831 | 2026-08-04 09:45:37 | 1 | |||||||||
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Guided Sparse Factor Analysis Resource Report Resource Website 1+ mentions |
Guided Sparse Factor Analysis (RRID:SCR_025023) | GSFA | software resource, software toolkit | Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data. | sparse factor analysis, differential gene expression, discovery simultaneously, single cell CRISPR screening data, | NIMH R01MH110531; NHGRI R01HG010773; NIMH R01MH116281; NIGMS R01 GM126553; NHGRI R01 HG011883; NSF ; Sloan Research Fellowship |
PMID:37770710 | Free, Available for download, Freely available | SCR_025023 | 2026-08-04 09:45:42 | 1 | ||||||||
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Conos Resource Report Resource Website 1+ mentions |
Conos (RRID:SCR_026381) | software resource, software toolkit, source code | Software R package for joint analysis of multiple single-cell RNA-seq datasets. Used to wire together large collections of single-cell RNA-seq datasets, which allows for both identification of recurrent cell clusters and propagation of information between datasets in multi-sample or atlas-scale collections. | joint analysis of multiple single-cell RNA-seq datasets, multiple single-cell RNA-seq datasets, identification of recurrent cell clusters, propagation of information between datasets, multi-sample, atlas-scale collections, | NHLBI R01HL131768; NSF ; Zimin Foundation |
DOI:10.1038/s41592-019-0466-z | Free, Available for download, Freely available | SCR_026381 | 2026-08-04 09:45:59 | 6 | |||||||||
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MeTPeak Resource Report Resource Website 10+ mentions |
MeTPeak (RRID:SCR_026533) | software resource, software toolkit, source code | Software package for finding the location of m6A sites in MeRIP-seq data. | finding location of m6A sites, MeRIP-seq data | NCI P30CA54174; NCI U54 CA113001; NIGMS R01 GM113245; Natural Science Foundation of China ; NSF |
PMID:27307641 | Free, Available for download, Freely available | SCR_026533 | 2026-08-04 09:46:01 | 10 | |||||||||
|
FARDEEP Resource Report Resource Website |
FARDEEP (RRID:SCR_026704) | FARDEEP | software application, software resource, source code | Software R tool for enumerating immune cell subsets from whole tumor tissue samples. Utilizes adaptive least trimmed square to automatically detect and remove outliers before estimating cell compositions. | enumerating immune cell subsets, whole tumor tissue samples, estimating cell compositions, | NIDCR R03 DE027399; NIDCR R01 DE026728; NIDCR R00 DE024173; NIDCR F31 DE028740; NSF ; Michigan State University STEM Gateway Fellowship ; University of Michigan Rogel Cancer Center Research Grant |
PMID:31059559 | Free, Available for download, Freely available | SCR_026704 | Fast And Robust DEconvolution of Expression Profiles | 2026-08-04 09:46:03 | 0 | |||||||
|
kraken2 Resource Report Resource Website 1000+ mentions |
kraken2 (RRID:SCR_026838) | software application, software resource, source code | Software tool as second version of Kraken taxonomic sequence classification system. | taxonomic sequence classification system, taxonomic, sequence, classification system, | NSF ; NIGMS R01 GM118568; NIGMS R35 GM130151 |
PMID:31779668 | Free, Available for download, Freely available | SCR_026838 | 2026-08-04 09:46:06 | 1107 | |||||||||
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PHATE Resource Report Resource Website 1+ mentions |
PHATE (RRID:SCR_027119) | data processing software, source code, software resource, software application, 3d visualization software, data visualization software | Software tool for visualizing high dimensional data using novel conceptual framework for learning and visualizing manifold to preserve both local and global distances. | visualizing high dimensional data, high dimensional data, | NICHD F31HD097958; NHGRI 1R01HG008383; NSF ; NIGMS R01GM107092; NIGMS R01GM130847 |
PMID:31796933 | Free, Available for download, Freely available, | SCR_027119 | Potential of Heat-diffusion for Affinity-based Transition Embedding | 2026-08-04 09:46:08 | 2 | ||||||||
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Northwestern University Central Laboratory for Materials Mechanical Properties Core Facility Resource Report Resource Website 1+ mentions |
Northwestern University Central Laboratory for Materials Mechanical Properties Core Facility (RRID:SCR_017877) | CLaMMP | access service resource, core facility, service resource | Core provides mechanical testing machines and accessories for conducting educational, research, and outreach experiments on most solid materials. | Material, mechanical, property, testing, solid, service, core, ABRF | is listed by: ABRF CoreMarketplace | NSF DMR 1720139 | Open | ABRF_727 | SCR_017877 | Central Laboratory for Materials Mechanical Properties | 2026-08-04 09:44:18 | 3 | ||||||
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University of California at Berkeley Cancer Research Laboratory Molecular Imaging Center Core Facility Resource Report Resource Website 50+ mentions |
University of California at Berkeley Cancer Research Laboratory Molecular Imaging Center Core Facility (RRID:SCR_017852) | MIC | access service resource, core facility, service resource | Microscopy core specializing in laser based fluorescence techniques. Offers training and expertise in 20 different microscope systems, including live cell and in vivo imaging, laser scanning (LSM) and spinning disk (SDC) confocal, multi-photon (2p), fluorescent lifetime imaging (FLIM), light-sheet microscopy (SPIM), super resolution (Airyscan), slide scanning and patterned illumination for optogenetic manipulation and readout. Provides offline computer analysis workstations for image processing, visualization and analysis, including GPU workstations. MIC operates in 3 different buildings on campus, with primary locations in Life Sciences Addition (LSA), North-side core in Barker Hall, and small outpost in Li Ka Shing Center for Biomedical and Health Sciences (LKS).Provides equipment in categories:Confocal and multi photon laser scanning microscopes,Spinning disk confocal microscopes,Lightsheet (SPIM) microscopes,Epifluorescence/widefield scopes and Computer workstations. | Molecular, imaging, microscopy, system, laser, based, fluorescent, technique, live, cell, in vivo, slide, scanning, image, processing, visualization, analysis, service, core | Helen Wills Neuroscience Institute ; NSF DBI1041078; Gordon and Betty Moore Foundation ; NCRR S10 RR028971; Biological Faculty Research Fund ; Fidelity Foundation Award ; NCRR S10 RR027696; NEI R01 EY015514; NSF DBI 0116016 |
Open | ABRF_659 | SCR_017852 | CRL Molecular Imaging Center | 2026-08-04 09:44:13 | 64 | |||||||
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Donald Danforth Plant Science Center Advanced Bioimaging Laboratory Core Facility Resource Report Resource Website 10+ mentions |
Donald Danforth Plant Science Center Advanced Bioimaging Laboratory Core Facility (RRID:SCR_018951) | access service resource, core facility, service resource | Core provides instruments for live cell imaging including Leica SP8-X confocal microscope and other fluorescence microscopes. Facility provides workstation for confocal image processing, ancillary equipment required for transmission electron microscopy. Services are provided as self services after user training by IMF staff or as full services done by core facility staff. | Live cell imaging, Leica SP8-X, confocal microscope, flulorescent microscope, confocal image processing, transmission electron microscopy, ABRF, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: Donald Danforth Plant Science Center |
NSF ; NIH |
ABRF_1026 | https://www.scienceexchange.com/labs/advanced-bioimaging-laboratory, https://coremarketplace.org/?FacilityID=1026 | SCR_018951 | Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center Integrated Microscopy Facility | 2026-08-04 09:44:29 | 20 | |||||||
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University of Colorado Boulder High Performance Computing PetaLibrary Core Facility Resource Report Resource Website 10+ mentions |
University of Colorado Boulder High Performance Computing PetaLibrary Core Facility (RRID:SCR_019299) | PetaLibrary | access service resource, core facility, service resource | Provides service to support storage, archival, and sharing of research data. Available at subsidized cost to any researcher affiliated with University of Colorado Boulder. | USEDit, ABRF, research data support storage, research data archival, research data sharing |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Colorado Boulder; Colorado; USA |
NSF ACI-1532235; NSF ACI-1532236 |
Restricted | ABRF_1097 | https://coremarketplace.org/?FacilityID=1097 | SCR_019299 | Colorado University at Boulder High Performance Computing PetaLibrary Core Facility, High Performance Computing - CU PetaLibrary, University of Colorado at Boulder High Performance Computing PetaLibrary Core Facility | 2026-08-04 09:44:32 | 22 | |||||
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James Madison University Light Microscopy and Imaging Core Facility Resource Report Resource Website 1+ mentions |
James Madison University Light Microscopy and Imaging Core Facility (RRID:SCR_021904) | access service resource, core facility, service resource | Core provides instrumentation, resources, training, and consultation. Facility offers access to diverse range of light microscope and imaging systems,image analysis software and solutions, practical and theoretical training for faculty, students and classes,consultation on data acquisition, analysis, and presentation. | USEDit, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: James Madison University |
NSF DBI 1725885; NSF DBI 0619207 |
open | ABRF_1259 | https://coremarketplace.org/?FacilityID=1259 | SCR_021904 | James Madison University JMU-Light Microscopy and Imaging Facility, JMU-Light Microscopy and Imaging Facility | 2026-08-04 09:44:54 | 3 | ||||||
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TCW Resource Report Resource Website 1+ mentions |
TCW (RRID:SCR_001875) | TCW | software resource | Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R. | transcript, assembly annotation, differential expression, transcript set, ortholog, expression, linux, java, mysql, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Arizona; Arizona; USA |
NSF IOS-1044821 | PMID:23874959 | Free, Available for download, Freely available | OMICS_01940, biotools:tCW | https://bio.tools/TCW | SCR_001875 | Transcriptome Computational Workbench, TCW: Transcriptome Computational Workbench | 2026-08-01 12:01:53 | 2 | ||||
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International Neuroinformatics Coordinating Facility Resource Report Resource Website 50+ mentions |
International Neuroinformatics Coordinating Facility (RRID:SCR_002282) | INCF | nonprofit organization | Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society. | neuroinformatics, neuroscience, neuroimaging, clinical, brain, data, sharing, reuse, global |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Spike Sorting Evaluation Project is related to: Allen Brain Atlas API is related to: SenseLab has parent organization: Karolinska Institute; Stockholm; Sweden has parent organization: Royal Institute of Technology; Stockholm; Sweden is parent organization of: INCF Dataspace is parent organization of: Waxholm Space is parent organization of: MUlti SImulation Coordinator is parent organization of: INCF Software Center is parent organization of: Program on Ontologies of Neural Structures is parent organization of: Common Upper Mammalian Brain Ontology is parent organization of: INCF Training in Neuroinformatics is parent organization of: INCF Funding is parent organization of: INCF Blog is parent organization of: INCForg - YouTube is parent organization of: INCF Swiss Node is parent organization of: INCF Newsroom is parent organization of: INCF Japan Node is parent organization of: Scalable Brain Atlas is parent organization of: INCF Job Board is parent organization of: INCF Neuroimaging Data Sharing is parent organization of: Waxholm Space is parent organization of: NeuroLex is parent organization of: Neuroimaging Data Model is parent organization of: Neuron Registry Curator Interface is parent organization of: INCF-Neurobot |
Swedish Research Council ; Swedish Foundation for Strategic Research ; NSF |
ISNI: 0000 0004 6107 939X, grid.498423.0, nif-0000-00365 | https://ror.org/02y5xjh56 | SCR_002282 | INCF, International Neuroinformatics Coordinating Facility, The International Neuroinformatics Coordinating Facility | 2026-08-01 12:02:09 | 56 | ||||||
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SobekCM Resource Report Resource Website |
SobekCM (RRID:SCR_003225) | SobekCM | software resource | Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories. | archiving, resource management, metadata standard, ontology, data repository, research object, c#, windows |
is listed by: FORCE11 has parent organization: University of Florida; Florida; USA has parent organization: Google Code has parent organization: SourceForge |
NEH ; NSF ; NHPRC ; IMLS |
Free, Available for download, Freely available | nlx_157266 | SCR_003225 | SobekCM Digital Repository Software, SobekCM : Digital Content Management System, SobekCM Digital Repository | 2026-08-01 12:02:28 | 0 | ||||||
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PHAST Resource Report Resource Website 50+ mentions |
PHAST (RRID:SCR_003204) | PHAST | software resource | A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code. | evolutionary genomic, evolution, genomics, sequence alignment, phylogenetic tree, genomic annotation, functional element, protein-coding exon, conserved sequence, phylogenetic modeling, ancestral sequence, c |
is listed by: OMICtools is listed by: Debian has parent organization: Cornell University; New York; USA |
NIH ; David and Lucile Packard Foundation ; NHGRI ; University of California Biotechnology Research and Education Program ; NSF DBI-0644111; NIGMS R01-GM082901-01 |
PMID:21278375 DOI:10.1093/bib/bbq072 |
Free, Available for download, Freely available | OMICS_01557 | https://sources.debian.org/src/phast/ | SCR_003204 | Phylogenetic Analysis with Space/Time Models | 2026-08-01 12:02:28 | 58 | ||||
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Adaptive Poisson-Boltzmann Solver Resource Report Resource Website 50+ mentions |
Adaptive Poisson-Boltzmann Solver (RRID:SCR_008387) | APBS | software resource | APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. It also provides implicit solvent models of nonpolar solvation which accurately account for both repulsive and attractive solute-solvent interactions. APBS uses FEtk (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FEtk is a portable collection of finite element modeling class libraries written in an object-oriented version of C. It is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. | software package, modeling, biomolecular, electrostatic, molecular, dynamics, binding energy, equilibrium, protein, ligand, solvation, kinetics, simulation, finite element |
is listed by: 3DVC is related to: Finite Element Toolkit has parent organization: Washington University in St. Louis; Missouri; USA |
IBM/American Chemical Society ; NPACI/San Diego Supercomputer Center ; W. M. Keck Foundation ; National Biomedical Computation Resource ; NSF ; NIH |
nif-0000-30035 | SCR_008387 | 2026-08-01 12:03:30 | 50 | ||||||||
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Jackal Resource Report Resource Website 10+ mentions |
Jackal (RRID:SCR_008665) | software resource | Jackal is a collection of programs designed for the modeling and analysis of protein structures. Its core program is a versatile homology modeling package. It contains twelve individual programs, each with their own function. | software, software repository, modeling, analysis, protein structure |
has parent organization: Columbia University; New York; USA has parent organization: Howard Hughes Medical Institute |
NSF DBI-9904841; NIGMS 5 R37 GM30518 |
Public, Free | nif-0000-33373 | SCR_008665 | 2026-08-01 12:03:59 | 14 | ||||||||
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Neurogrid Resource Report Resource Website 10+ mentions |
Neurogrid (RRID:SCR_005024) | Neurogrid | instrument resource | A specialized hardware platform that will perform cortex-scale emulations while offering software-like flexibility. With sixteen 12x14 sq-mm chips (Neurocores) assembled on a 6.5x7.5 sq-in circuit board that can model a slab of cortex with up to 16x256x256 neurons - over a million! The chips are interconnected in a binary tree by 80M spike/sec links. An on-chip RAM (in each Neurocore) and an off-chip RAM (on a daughterboard, not shown) softwire vertical and horizontcal cortical connections, respectively. It provides an affordable option for brain simulations that uses analog computation to emulate ion-channel activity and uses digital communication to softwire synaptic connections. These technologies impose different constraints, because they operate in parallel and in serial, respectively. Analog computation constrains the number of distinct ion-channel populations that can be simulatedunlike digital computation, which simply takes longer to run bigger simulations. Digital communication constrains the number of synaptic connections that can be activated per secondunlike analog communication, which simply sums additional inputs onto the same wire. Working within these constraints, Neurogrid achieves its goal of simulating multiple cortical areas in real-time by making judicious choices. | simulation, neuron, cortex, synapse, analog vlsi, instrument, equipment, hardware | has parent organization: Stanford University; Stanford; California | NSF ; NIH |
PMID:17959490 | nlx_97879 | SCR_005024 | 2026-08-01 12:02:52 | 14 | |||||||
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WHAM Resource Report Resource Website 100+ mentions |
WHAM (RRID:SCR_005497) | WHAM | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. High-throughput sequence alignment tool that aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bps reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques. Feature list for the current version (v 0.1.5) of WHAM: * Supports paired-end reads * Supports up to 5 errores * Supports alignments with gaps * Supports quality scores for filtering invalid alignments, and sorting valid alignments * finds ALL valid alignments * Supports multi-threading * Supports rich reporting modes * Supports SAM format output | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
Facebook ; NSF IIS-1110948 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00697, biotools:wham | https://bio.tools/wham, https://sources.debian.org/src/wham-align/ | SCR_005497 | Wisconsin?s High-throughput Alignment Method | 2026-08-01 12:02:55 | 345 |
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