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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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riboWaltz Resource Report Resource Website 10+ mentions |
riboWaltz (RRID:SCR_016948) | software application, data processing software, data visualization software, data analysis software, software resource | Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates. | calculation, optimal, Psite, offset, diagnostic, analysis, visual, inspection, ribosome, profiling, data, read, alignment, transcript, coordinate |
uses: ggplot2 uses: Biostrings uses: GenomicFeatures uses: GenomicRanges uses: IRanges uses: devtools is related to: R Project for Statistical Computing |
Autonomous Province of Trento ; Wellcome Trust |
PMID:30102689 | Free, Available for download, Freely available | SCR_016948 | 2026-02-16 09:49:07 | 21 | ||||||||
|
Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | data analysis service, analysis service resource, web application, software resource, production service resource, service resource | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/ https://bio.tools/pavian |
SCR_016679 | 2026-02-16 09:49:05 | 22 | ||||||
|
NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | software application, data processing software, data visualization software, data analysis software, image analysis software, software resource | Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures. | biological, image, data, visualization, analysis, tracing, single, neuron, 3D, structure, brain |
is listed by: OMICtools is listed by: CRAN is related to: R Project for Statistical Computing is related to: elmr has parent organization: University of Cambridge; Cambridge; United Kingdom |
DOI:10.5281/zenodo.10171 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/nat/index.html |
SCR_016716 | NeuroAnatomy Toolbox, neuroanatomy toolbox, Neuro Anatomy Toolbox, neuro anatomy toolbox | 2026-02-16 09:49:05 | 5 | ||||||
|
BBmap Resource Report Resource Website 500+ mentions |
BBmap (RRID:SCR_016965) | software application, data processing software, software toolkit, image analysis software, software resource, alignment software | Software tool as a short read aligner for DNA and RNA seq data. Used for large genomes with millions of scaffolds. Can align reads from Illumina, PacBio, 454, Sanger, Ion Torrent, Nanopore. Fast and accurate, particularly with highly mutated genomes or reads with long indels, even whole gene deletions over 100kbp long. It has no upper limit to genome size or number of contigs. Written in Java, can run on any platform. | Joint Genome Institute, short, read, aligner, DNA, RNA, sequencing, data, large, genome, scaffold, mutated, long, indel |
is listed by: Bestus Bioinformaticus Tools is listed by: Debian is related to: University of California at Berkeley; Berkeley; USA |
Free, Available for download, Freely available | https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/ https://sources.debian.org/src/bbmap/ |
SCR_016965 | 2026-02-16 09:49:08 | 797 | |||||||||
|
BD FACS Sortware sorter software Resource Report Resource Website 1+ mentions |
BD FACS Sortware sorter software (RRID:SCR_016722) | BD FACS Sortware software | software application, data processing software, data visualization software, data analysis software, software resource | Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems. | control, cell, sorter, acquisition, analysis, integrate, data, instrument, system, Becton Dickinson and Company | Commercially available | SCR_016722 | , BD FACS Sortware, Becton Dickinson FACS Sortware, BD FACS Sortware software | 2026-02-16 09:49:05 | 5 | |||||||||
|
TopDom Resource Report Resource Website 10+ mentions |
TopDom (RRID:SCR_016964) | TOPDOM | software application, data processing software, software toolkit, data analysis software, software resource | Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, topological, domain, genome, structure, linear, time, data, analysis |
has parent organization: University of Southern California; Los Angeles; USA works with: CCTOP |
NHLBI U01 HL108634; NIDDK U54 DK107981; NSF CAREER 0747475; NSF CAREER 1150287; Arnold and Mabel Beckman foundation ; Pew Charitable Trusts |
PMID:26704975 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016964 | TOPological DOMains, Topological Domains, TopDom_v0.0.2, TopDom_v0.0.1 | 2026-02-16 09:49:08 | 10 | ||||||
|
VectorMap Resource Report Resource Website 10+ mentions |
VectorMap (RRID:SCR_016721) | web service, data access protocol, data repository, database, storage service resource, software resource, portal, service resource, data or information resource | Collection of disease maps, and mapped collection data and distribution models for arthropod disease vector species, including mosquitoes, ticks, sand flies, mites, and fleas, as well as the hosts/reservoirs of vector-borne disease pathogens. VectorMap is modeled after MosquitoMap. | disease, map, collection, data, distribution, model, arthropod, disease, vector, species | has parent organization: Walter Reed Biosystematics Unit | arthropod disease | US Department of Defense Global Emerging Infections Surveillance and Response System ; Division of the Armed Forces Health Surveillance Center ; Global Biodiversity Information System |
Public, Free, Available for download, Freely available, Acknowledgement requested, Tutorial available | SCR_016721 | 2026-02-16 09:49:05 | 22 | ||||||||
|
Prevention of Lower Urinary Tract Symptoms Resource Report Resource Website |
Prevention of Lower Urinary Tract Symptoms (RRID:SCR_016923) | PLUS | data or information resource, organization portal, consortium, portal | Research consortium from many different fields to plan, perform and analyze the studies that are needed to help researchers conduct future prevention and intervention for Lower Urinary Tract Symptoms (LUTS) in women. | plan, perform, analyze, data, prevent, lower, urinary, track, symptom, women |
is listed by: NIDDK Information Network (dkNET) is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology is related to: University of Minnesota Medical School; Minnesota; USA |
NIDDK | SCR_016923 | Prevention of Lower Urinary Tract Symptoms, Prevention LUTS, PLUS | 2026-02-16 09:49:07 | 0 | ||||||||
|
The Human BioMolecular Atlas Program Resource Report Resource Website 10+ mentions |
The Human BioMolecular Atlas Program (RRID:SCR_016922) | HuBMAP | funding resource, data or information resource, project portal, portal | Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows. | organism, cell, tissue, data, generation, technology, organization, functional, mapping, human, body |
uses: Azimuth is listed by: NIDDK Information Network (dkNET) is related to: HuBMAP Data Portal |
NIH | https://humanatlas.io/omap https://avr.hubmapconsortium.org/ https://commonfund.nih.gov/HuBMAP https://zenodo.org/records/5244551 |
SCR_016922 | Human BioMolecular Atlas Program, HuBMAP, The Human BioMolecular Atlas Program, NIH HuBMAP | 2026-02-16 09:49:07 | 22 | |||||||
|
Digital Expression Explorer 2 Project Resource Report Resource Website 1+ mentions |
Digital Expression Explorer 2 Project (RRID:SCR_016929) | DEE2 | project portal, data repository, database, storage service resource, portal, service resource, data or information resource | Software tool as a repository of uniformly processed RNA-seq data mined from public data obtained from NCBI Short Read Archive . DEE2 consists of three parts: Webserver where end-users can search for and obtain data-sets of interest, Pipeline that can download and process SRA data as well as users own fastq files, Back-end that collects, filters and organises data provided by contributing worker nodes. | transcriptome, database, RNA-seq, sequencing, processed, data |
is related to: Digital Expression Explorer 2 Source Code is related to: Digital Expression Explorer 2 Docker Image |
DOI:10.5281/zenodo.1561840 | Free, Freely available | SCR_016929 | DEE2 Project | 2026-02-16 09:49:07 | 4 | |||||||
|
Thunder STORM Resource Report Resource Website 10+ mentions |
Thunder STORM (RRID:SCR_016897) | ThunderSTORM | software application, data processing software, software toolkit, data analysis software, software resource | Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging. | automated, processing, analysis, visualization, data, acquired, single, molecule, localization, microscopy, SMLM, imaging, bio.tools |
is listed by: Debian is listed by: bio.tools is a plug in for: ImageJ |
Czech Science Foundation ; Charles University ; European Regional Development Fund ; European Social Fund |
PMID:24771516 | Free, Available for download, Freely available | biotools:thunderstorm | https://bio.tools/thunderstorm | SCR_016897 | 2026-02-16 09:49:07 | 42 | |||||
|
CCTop Resource Report Resource Website 100+ mentions |
CCTop (RRID:SCR_016890) | software application, data processing software, data analysis software, software resource, web application, service resource | Web tool for CRISPR/Cas9 target prediction. Identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation. | CRISPR, Cas9, target, prediction, sgRNA, site, data | is related to: Python Programming Language | European Research Council ; German Research Foundation |
PMID:25909470 | SCR_016890 | 2026-02-16 09:49:07 | 110 | |||||||||
|
EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | data processing software, software application, software resource, image processing software | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | EMAN1, EMAN2 | 2026-02-16 09:49:06 | 106 | |||
|
Metab Resource Report Resource Website 1+ mentions |
Metab (RRID:SCR_016877) | Metab | software application, data processing software, software toolkit, data analysis software, software resource | Software package as a metabolomic data processing pipeline in R codes. | metabolomic, data, processing, pipeline, analysis, datasets | Health Research Council of New Zealand | DOI:10.1093/bioinformatics | Free, Available for download, Freely available | https://bioconductor.org/packages/release/bioc/html/Metab.html | SCR_016877 | Metabolome, Metab 1.0 | 2026-02-16 09:49:07 | 1 | ||||||
|
OpenBMI Resource Report Resource Website 1+ mentions |
OpenBMI (RRID:SCR_016876) | software application, data processing software, software toolkit, data visualization software, data analysis software, software resource | Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time. | brain, computer, interface, analysis, signal, acquire, filter, process, visualize, data | has parent organization: Korea University; Seoul; South Korea | Free, Available for download, Freely available | http://openbmi.org/ | SCR_016876 | 2026-02-16 09:49:06 | 5 | |||||||||
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KnowEnG Resource Report Resource Website 1+ mentions |
KnowEnG (RRID:SCR_016875) | training resource, organization portal, software resource, portal, data or information resource | Part of the NIH Big Data to Knowledge (BD2K) Initiative. One of 11 Centers of Excellence in Big Data Computing. Platform for genomics data analysis where user-supplied data sets will be analyzed in the context of existing knowledge. E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data. | center, excellence, big, data, computing, biomedical, analytics |
has parent organization: Mayo Clinic has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIGMS U54 GM114838 | PMID:26205246 | https://github.com/BD2K/KnowEng | SCR_016875 | Knowledge Engine for Genomics, The Knowledge Engine for Genomics | 2026-02-16 09:49:06 | 1 | |||||||
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clusterProfiler Resource Report Resource Website 10000+ mentions |
clusterProfiler (RRID:SCR_016884) | software application, data processing software, data visualization software, data analysis software, software resource | Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters. | data, statistical, analysis, visualization, gene, cluster, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
National 973 Projects of China ; 2007 Chang-Jiang Scholars Program ; National Natural Science Foundation of China ; Guangdong Natural Science Research Grant ; Fundamental Research Funds for the Central Universities |
PMID:22455463 | Free, Available for download, Freely available | biotools:clusterprofiler | https://github.com/GuangchuangYu/clusterProfiler https://guangchuangyu.github.io/software/clusterProfiler/ https://bio.tools/clusterprofiler |
SCR_016884 | Cluster Profiler | 2026-02-16 09:49:07 | 10762 | |||||
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Kidney Precision Medicine Project Resource Report Resource Website 50+ mentions |
Kidney Precision Medicine Project (RRID:SCR_016920) | KPMP | the community can contribute to this resource, availability annotation standard, nif annotation standard, organization portal, narrative resource, project portal, topical portal, consortium, portal, data or information resource, standard specification, disease-related portal | Project to ethically obtain and evaluate human kidney biopsies from participants with Acute Kidney Injury (AKI) or Chronic Kidney Disease (CKD), create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways, and targets for novel therapies. Used to develop the next generation of software tools to visualize and understand the various components of kidney diseases and to optimize data collection. Multi site collaboration comprised of patients, clinicians, and investigators from across the United States. | ethically, obtain, evaluate, human, kidney, biopsy, collaboration, patient, clinician, researcher, acute, injury, chronic, disease, tissue, atlas, cell, pathway, target, novel, therapy, data, collection |
is listed by: NIDDK Information Network (dkNET) is related to: Kidney Tissue Atlas |
Acute Kidney Injury, Chronic Kidney Disease | NIDDK | Open resource for academics, industry, and the broader scientific community | SCR_016920 | Kidney Precision Medicine Project, The Kidney Precision Medicine Project | 2026-02-16 09:49:07 | 53 | ||||||
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Bestus Bioinformaticus Duk Resource Report Resource Website 100+ mentions |
Bestus Bioinformaticus Duk (RRID:SCR_016969) | BBDuk | software application, data processing software, data analytics software, data analysis software, software resource | Software tool for trimming and filtering sequencing data. Used to combine data quality related trimming, filtering, and masking operations into a single tool adapter. BBDuk2 allows multiple kmer based operations in a single pass. | sequencing, data, quality, trimming, filtering, masking, operation, single, tool, adapter, contaminant, sequence, GC, length, entropy, format, conversion, histogram, kmer, estimation, decontamination |
is listed by: Bestus Bioinformaticus Tools has parent organization: DOE Joint Genome Institute works with: Reformat |
http://seqanswers.com/forums/showthread.php?t=42776 https://www.geneious.com/plugins/bbduk/#links |
SCR_016969 | BB Duk, Decontamination Using Kmers, Bestus Bioinformaticus Decontamination using kmers, BBDuk2, BBDUK, BBDuk, BBDuk 2, Bestus Bioinformaticus Decontamination Using kmers | 2026-02-16 09:49:08 | 184 | ||||||||
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Walter Reed Biosystematics Unit Resource Report Resource Website 1+ mentions |
Walter Reed Biosystematics Unit (RRID:SCR_016729) | WRBU | data or information resource, topical portal, organism-related portal, portal | National resource for systematics research on medically important arthropods and maintainance of the U.S. mosquito collection based in the Smithsonian Institution. Provides an online repository for vector collection data and clearinghouse where individuals and organizations can contribute vector occurrence records, search for vector information, and use tools for the visualization of various vector collections. | medically, important, arthropods, maintanace, repository, U.S. mosquito, data, vector, collection | is parent organization of: VectorMap | SCR_016729 | The Walter Reed Biosystematics Unit, WRBU, Walter Reed Biosystematics Unit | 2026-02-16 09:49:05 | 5 |
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