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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SomaticSignatures Resource Report Resource Website 1+ mentions |
SomaticSignatures (RRID:SCR_025620) | source code, software resource, software toolkit | Software R package for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments. | R, identifying mutational signatures, single nucleotide variants, high-throughput experiments, | NSF | PMID:26163694 | Free, Available for download, Freely available, | https://github.com/juliangehring/SomaticSignatures | SCR_025620 | 2026-02-17 10:04:23 | 4 | ||||||||
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MorphoSource Resource Report Resource Website 10+ mentions |
MorphoSource (RRID:SCR_025654) | data or information resource, database | Publicly accessible 3D data repository where subject experts, educators, and general public can find, view, interact with, and download 3D and 2D media representing physical objects important to the world’s natural history, cultural heritage, and scientific collections. Media data are contributed by a community that includes museums, institutions, researchers, scholars, and other subject experts who use MorphoSource to archive data, share findings, and increase scholarly impact. Contributed media represent both biological objects such as fossils and representatives of living species, as well as artifacts and objects created by humans that are critical to our shared cultural heritage. | 3D media, 2D media, physical objects, natural history, cultural heritage, scientific collections, shared cultural heritage, | NSF ; Duke University |
Free, Freely available, | r3d100012224 | https://github.com/MorphoSource https://doi.org/10.17616/R35Q0K |
SCR_025654 | 2026-02-17 10:04:23 | 48 | ||||||||
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Conos Resource Report Resource Website 1+ mentions |
Conos (RRID:SCR_026381) | source code, software resource, software toolkit | 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 | 2026-02-17 10:05:05 | 6 | |||||||||
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MeTPeak Resource Report Resource Website 10+ mentions |
MeTPeak (RRID:SCR_026533) | source code, software resource, software toolkit | 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 | 2026-02-17 10:05:06 | 10 | |||||||||
|
FARDEEP Resource Report Resource Website |
FARDEEP (RRID:SCR_026704) | FARDEEP | software application, source code, software resource | 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 | 2026-02-17 10:05:07 | 0 | |||||||
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kraken2 Resource Report Resource Website 1000+ mentions |
kraken2 (RRID:SCR_026838) | software application, source code, software resource | 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 | 2026-02-17 10:05:26 | 1107 | |||||||||
|
PHATE Resource Report Resource Website 1+ mentions |
PHATE (RRID:SCR_027119) | 3d visualization software, software application, data processing software, source code, software resource, 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 | 2026-02-17 10:05:28 | 2 | ||||||||
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VenomView Resource Report Resource Website |
VenomView (RRID:SCR_027588) | software application, web application, software resource, standalone software | Open-access, browser-based visualization and summary tool for venom transcriptomic and proteomic data. R Shiny–based interactive application designed as visualization and reporting interface for venom transcriptomic and proteomic data. It enables users to explore annotation metrics, toxin gene families, and quality-control summaries generated by analysis pipelines. While it will eventually serve as part of the VenomsBase front end, VenomView currently operates as standalone prototype. Provides interactive dashboards showing assembly quality, annotation scores, toxin gene families, and functional domains generated by the VenomFlow analysis pipeline. Connected to VenomLanding, VenomView currently features Doryteuthis pealeii (Squid), linking metadata with detailed annotation summaries. The expanded version will include Sepia bandensis (Cuttlefish), Octopus bimaculoides, and arachnid species. | R Shiny–based interactive application, visualization and reporting interface, venom transcriptomic and proteomic data, |
uses: Shiny has parent organization: Harvard University; Cambridge; United States |
NSF | SCR_027588 | 2026-02-17 10:04:46 | 0 | ||||||||||
|
Nested containment list Resource Report Resource Website |
Nested containment list (RRID:SCR_027849) | NCLS, NCList | software library, software resource, software toolkit | Software library for nested containment list data structure for interval overlap queries, like interval tree. It is a static interval-tree that is fast for both construction and lookups. | nested containment list data structure, interval overlap queries, static interval-tree, construction and lookups, | NCRR U54 RR021813; NSF |
PMID:17234640 | Free, Available for download, Freely available | SCR_027849 | , Nested Containment List (NCList), Nested Containment List | 2026-02-17 10:05:31 | 0 | |||||||
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T Cell ExTRECT Resource Report Resource Website |
T Cell ExTRECT (RRID:SCR_027742) | source code, software resource, software toolkit | Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes. | T-cell, T cell receptor excision circle, WES data, hg19 or hg38 aligned genomes, | NHLBI U54HL108460; NCATS UL1TR000100; NCI R21CA177519; NCI P30CA023100; NCI U01CA196406; NLM T15LM011271; NIH Office of the Director DP5OD017937; NSF |
PMID:34497419 | Free, Available for download, Freely available | SCR_027742 | , T cell exome TREC, T cell exome T cell Receptor Excision Circle | 2026-02-17 10:05:29 | 0 | ||||||||
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CoMUT Resource Report Resource Website 1+ mentions |
CoMUT (RRID:SCR_027745) | software library, source code, software resource, software toolkit | Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots. | genomic DNA, phenotype, visualizing genomic and phenotypic information, comutation plots, | NSF ; NIGMS T32 GM008313; NCI R37 CA222574; NCI R01 CA227388; NCI U01 CA233100 |
PMID:32502231 | Free, Available for download, Freely available | SCR_027745 | 2026-02-17 10:04:51 | 2 | |||||||||
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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 | 2026-02-14 02:01:43 | 14 | ||||||||
|
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 | 2026-02-14 02:01:33 | 50 | ||||||||
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SVM-fold: Protein Fold Prediction Resource Report Resource Website |
SVM-fold: Protein Fold Prediction (RRID:SCR_006834) | SVM-fold | service resource | This web server makes predictions of family, superfamily and fold level classifications of proteins based on the Structural Classification of Proteins (SCOP) hierarchy using the Support Vector Machine (SVM) learning algorithm. SVM-FOLD detects subtle protein sequence similarities by learning from all available annotated proteins, as well as utilizing potential hits as identified by PSI-BLAST. Predictions of classes of proteins that do not have any known example with a significant pairwise PSI-BLAST E-value can still be found using SVMs. | has parent organization: University of Washington; Seattle; USA | NIGMS GM74257-01; NSF EIA-0312706 |
nlx_17631 | http://svm-fold.c2b2.columbia.edu/ | SCR_006834 | SVM-fold, Support Vector Machine fold | 2026-02-14 02:01:14 | 0 | |||||||
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DynGO Resource Report Resource Website 1+ mentions |
DynGO (RRID:SCR_007009) | DynGO | software resource | DynGO is a client-server application that provides several advanced functionalities in addition to the standard browsing capability. DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations (which requires more disk and memory to handle the semantic retrieval). The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples. Requirements: Java Platform: Windows compatible, Linux compatible, Unix compatible | gene, annotation, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology |
NSF IIS-0430743 | PMID:16091147 | Free for academic use | nlx_149118 | http://gauss.dbb.georgetown.edu/liblab | SCR_007009 | DynGO: a tool for visualizing and mining of Gene Ontology and its associations | 2026-02-14 02:01:26 | 6 | ||||
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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 | 2026-02-14 02:01:07 | 345 | |||||
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NESCent - National Evolutionary Synthesis Center Resource Report Resource Website 1+ mentions |
NESCent - National Evolutionary Synthesis Center (RRID:SCR_005911) | NESCent | institution | The National Evolutionary Synthesis Center (NESCent) is a nonprofit science center dedicated to cross-disciplinary research in evolution. NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries. Synthetic research in evolutionary science takes many forms but includes integrating novel data sets and models to address important problems within a discipline, developing new analytical approaches and tools, and combining methods and perspectives from multiple disciplines to answer and even create new fundamental scientific questions. NESCent facilitates such synthetic research by providing an environment for fertile interactions among scientists. Our Science and Synthesis program sponsors postdoctoral fellows and sabbatical scholars as resident scientists, and two kinds of meetings, working groups and catalysis meetings. Catalysis meetings provide a novel mechanism for bringing together diverse research communities and cultures to identify common interests, while working groups provide an opportunity for scientists to work together intensively on fundamental synthetic questions over a several-year period. These activities are community driven through our application process and evaluated by an external advisory board. Our Informatics program provides state of the art informatics tools to visiting and in-house scientists and aims to take the lead in assembling novel databases and developing new analytical tools for evolutionary biology. Finally it is sponsoring a major initiative to provide a digital data repository for work in evolutionary biology. NESCent''s Education and Outreach group communicates the results of evolutionary biology research to the general public and scientific community, provides outreach to groups who are underrepresented in evolutionary biology and works to improve evolution education. | evolution, evolutionary biology |
has parent organization: Duke University; North Carolina; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: North Carolina State University; North Carolina; USA is parent organization of: FEED is parent organization of: Phenoscape Knowledgebase is parent organization of: TreeBASE is parent organization of: Dryad Digital Repository |
NSF EF-0905606 | Wikidata: Q6972505, ISNI: 0000 0000 9027 3547, nlx_149487, grid.419343.8, Crossref funder ID: 100007514 | https://ror.org/001ykb961 | SCR_005911 | National Evolutionary Synthesis Center | 2026-02-14 02:01:11 | 7 | ||||||
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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 | 2026-02-14 02:00:13 | 2 | ||||
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InterNano Process Database Resource Report Resource Website 1+ mentions |
InterNano Process Database (RRID:SCR_013719) | InterNano | Database and knowledge base of techniques for processing nanoscale materials, devices, and structures that includes step-by-step descriptions, images, notes on methodology and environmental variables, and associated references and patent information. The purpose of the Process Database is to facilitate the sharing of appropriate process knowledge across laboratories.The processes included here have been previously published or patented | nanoscale, process knowledge, nanomanufacturing | has parent organization: University of Massachusetts Amherst; Massachusetts; USA | Division of Civil Mechanical and Manufacturing Innovation ; NSF 1025020 |
Free, Public | SCR_013719 | InterNano Resources for Nano Manufacturing | 2026-02-14 02:02:33 | 2 | ||||||||
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TAIR Resource Report Resource Website 5000+ mentions |
TAIR (RRID:SCR_004618) | TAIR, AGI LocusCode | data or information resource, database | Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided. | genetic, molecular biology, gene, genome, structure, product, metabolism, gene expression, dna, seed stock, genome map, genetic marker, physical marker, genome sequence, gene product, blast, experimental protocol, gold standard |
is used by: NIF Data Federation is listed by: OMICtools is listed by: re3data.org is listed by: DataCite is related to: AmiGO is related to: Saskatoon Arabidopsis T-DNA mutant population SK Collection is related to: CLENCH has parent organization: Carnegie Institution for Science is parent organization of: TAIR Keyword Browser is parent organization of: PubSearch |
NSF DBI-0850219; corporate and nonprofit organizations |
PMID:22140109 PMID:17986450 PMID:12444417 PMID:12519987 PMID:18287693 |
r3d100010185, nlx_61477, OMICS_01662 | https://doi.org/10.17616/R3QW21 | SCR_004618 | AGI LocusCode, The Arabidopsis Information Resource | 2026-02-14 02:00:59 | 7421 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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