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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
circular statistics Resource Report Resource Website 10+ mentions |
circular statistics (RRID:SCR_016651) | CircStat | data analysis software, data processing software, software application, software resource | Software toolbox for MATLAB for the descriptive and inferential statistical analysis of directional data. | circular, inferential, statistics, directional, data |
has parent organization: Max Planck Institute for Biological Cybernetics; Tubingen; Germany works with: MATLAB |
German Ministry of Education ; Science ; Research and Technology ; German National Academic Foundation |
DOI:10.18637/jss.v031.i10 | Free, Available for download, Registration required to MathWorks Account, | https://github.com/circstat/circstat-matlab | SCR_016651 | Matlab Circular Statistics Toolbox, , circstat-matlab, circular statistics, Circular Statistics, CircStat for Matlab | 2026-09-12 12:58:42 | 47 | |||||
|
MetaXpress Resource Report Resource Website 500+ mentions |
MetaXpress (RRID:SCR_016654) | data acquisition software, data processing software, image acquisition software, image analysis software, software application, software resource | Software tool for multi level analysis of applications optimized for ImageXpress instruments. High-content image analysis software featuring time lapse analysis. Used for 2D and 3D imaging. | Molecular Devices, ImageXpress, high, content, image, analysis, acquisition, time, lapse, 2D, 3D, cellular, imaging | Commercially available | SCR_016654 | 2026-09-12 12:58:42 | 657 | |||||||||||
|
Genotate Resource Report Resource Website |
Genotate (RRID:SCR_016659) | data access protocol, data or information resource, database, software resource, web service | Platform as a web-based interactive environment to automatically identify, explore and visualize homology and functional annotations for assembled transcripts. | identify, explore, visualize, homology, functional, annotation, assemble, transcript, dataset |
works with: Ensembl works with: UniProt works with: NONCODE |
ANR | Free, Available for download, Freely available, | SCR_016659 | 2026-09-12 12:58:43 | 0 | |||||||||
|
XYalign Resource Report Resource Website 1+ mentions |
XYalign (RRID:SCR_016661) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data. | correct, technical, bias, sex, chromosome, next, generation, sequencing, data | is listed by: OMICtools | NIGMS R35 GM124827 | DOI:10.1101/346940 | Free, Available for download, Freely available | SCR_016661 | 2026-09-12 12:58:43 | 1 | ||||||||
|
LoomPy Resource Report Resource Website 10+ mentions |
LoomPy (RRID:SCR_016666) | LoomPy | data processing software, data storage software, software application, software library, software resource, software toolkit | Python implementation of the Loom file format to store and organize very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations and sparse graph objects. Used to store single-cell gene expression data. Official Python library (API) used to create, read, and manipulate .loom files, supporting out-of-memory operations to handle datasets larger than RAM. | Python, Loom file, format, store, organize, omics, dataset, single, cell, expression, data, HDF5 |
is used by: BICCN works with: loom-viewer works with: Loom |
Free, Available for download, Freely available | https://linnarssonlab.org/loompy/, https://github.com/linnarsson-lab/loompy | SCR_016666 | Loompy v2.0, Loompy v2.0.14, Loom Python, LoomPy, LoomPython | 2026-09-12 12:58:43 | 40 | |||||||
|
Centrifuge Classifier Resource Report Resource Website 10+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
NHGRI R01 HG006677; NIGMS R01 GM083873; NSF ABI1356078; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge, https://bio.tools/centrifuge, https://sources.debian.org/src/centrifuge/ | SCR_016665 | 2026-09-12 12:58:43 | 10 | ||||||
|
PaVE Resource Report Resource Website 100+ mentions |
PaVE (RRID:SCR_016599) | PaVE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource, web application | Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information. | data, curated, papilloma, virus, genomic, sequence, analysis, storage, annotation, FASEB list | is listed by: NIAID | NIAID ZIA AI001071 | PMID:28053164 | Open source | SCR_016599 | PapillomaVirus Episteme, Papillomavirus Episteme | 2026-09-12 12:58:42 | 156 | ||||||
|
transfer_ learning_ ccnn Resource Report Resource Website 1+ mentions |
transfer_ learning_ ccnn (RRID:SCR_016590) | ccnn | data analysis software, data processing software, software application, software resource | Software program to implement transfer learning for a connectome convolutional neural network trained to classify functional connectomes using Tensorflow. | transfer, learning, connectome, convolutional, neural, network, functional, connectome, Tensorflow | uses: tensorflow | Free, Available for download, Freely available | SCR_016590 | connectome convolutional neural network, Connectome Convolutional Neural Network, CCNN | 2026-09-12 12:58:42 | 1 | ||||||||
|
TB PORTALS Resource Report Resource Website 10+ mentions |
TB PORTALS (RRID:SCR_016594) | consortium, data or information resource, data repository, disease-related portal, organization portal, portal, service resource, storage service resource, topical portal | Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data. | collect, data, sharing, analysis, tuberculosis, global, bio.tools |
is listed by: NIAID is listed by: bio.tools is listed by: Debian |
tuberculosis | NIH | DOI:10.1128/JCM.01013-17 | Free, Freely available | r3d100013925, biotools:TB_Portals | https://bio.tools/TB_Portals, https://doi.org/10.17616/R31NJN8L | SCR_016594 | 2026-09-12 12:58:42 | 20 | |||||
|
NMRProcFlow Resource Report Resource Website 10+ mentions |
NMRProcFlow (RRID:SCR_016592) | data processing software, data visualization software, software application, software resource | Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics. | NMR, metabolomics, data, viewer, spectra, processing, graphical, interface, bio.tools |
uses: R Project for Statistical Computing is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
French National Infrastructure in Metabolomics and Fluxomics | DOI:10.1007/s11306-017-1178-y | Free, Available for download, Freely available | biotools:nmrprocflow, SCR_022777 | https://github.com/INRA/NMRProcFlow, https://bio.tools/nmrprocflow, https://github.com/inra/nmrprocflow | SCR_016592 | Nuclear Magnetic Resonance PROcessing FLOW, Nuclear Magnetic Resonance Processing Flow | 2026-09-12 12:58:42 | 29 | |||||
|
BLASTClust Resource Report Resource Website 50+ mentions |
BLASTClust (RRID:SCR_016641) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets. | cluster, protein, nucleotide, sequence, pairwise, match, sequence |
is listed by: SoftCite has parent organization: NCBI works with: NCBI BLAST |
Free, Freely available | SCR_016641 | 2026-09-12 12:58:42 | 94 | ||||||||||
|
CheckM Resource Report Resource Website 100+ mentions |
CheckM (RRID:SCR_016646) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes by using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. | assess, quality, microbial, genome, recovered, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/gr.186072.114 | Free, Available for download, Freely available | biotools:checkm | https://github.com/Ecogenomics/CheckM, https://bio.tools/checkm | SCR_016646 | 2026-09-12 12:58:42 | 238 | |||||||
|
Genotyping Resource Report Resource Website 10+ mentions |
Genotyping (RRID:SCR_016645) | data access protocol, data analysis software, data processing software, sequence analysis software, software application, software resource, web service | Web tool to identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus. | identify, genotype, viral, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI works with: NCBI BLAST |
Free, Freely available | biotools:ncbi_genotyping | https://bio.tools/ncbi_genotyping | SCR_016645 | 2026-09-12 12:58:42 | 40 | ||||||||
|
Open Reading Frame Finder Resource Report Resource Website 1000+ mentions |
Open Reading Frame Finder (RRID:SCR_016643) | ORF finder | analysis service resource, data analysis software, data processing software, production service resource, sequence analysis software, service resource, software application, software resource | Software tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long. | search, open, reading, frame, DNA, sequence, ORF, protein, translation, data, encoding, segment, verify |
uses: BLASTP has parent organization: NCBI |
Free, Available for download, Freely available | SCR_016643 | Open Reading Frame finder, Open Reading Frame Finder | 2026-09-12 12:58:42 | 1955 | ||||||||
|
TRIAGE Resource Report Resource Website 1+ mentions |
TRIAGE (RRID:SCR_016609) | TRIAGE | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | Platform to facilitate prediction, analysis, and hypothesis generation from genome wide perturbation studies like those designed with RNAi and CRISPR technologies. | prediction, analysis, hypothesis, generation, genome, perturbation, study, RNAi, CRISP | is listed by: NIAID | NIH | Free, Available for download, Freely available | SCR_016609 | Throughput Ranking by Iterative Analysis of Genomic Enrichment | 2026-09-12 12:58:42 | 1 | |||||||
|
Libra Resource Report Resource Website |
Libra (RRID:SCR_016608) | data analysis software, data analytics software, data processing software, sequence analysis software, software application, software resource | Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples. | gene, distance, matrix, computation, k-mer-based, sequence, comparison, Hadoop, metagenomic, sample, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF 1640775 | Free, Available for download, Freely available | biotools:Libra_k-mer | https://bio.tools/Libra_k-mer | SCR_016608 | 2026-09-12 12:58:42 | 0 | |||||||
|
Walter Reed Biosystematics Unit Resource Report Resource Website 1+ mentions |
Walter Reed Biosystematics Unit (RRID:SCR_016729) | WRBU | data or information resource, organism-related portal, portal, topical 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 | 2026-09-12 12:58:44 | 5 | |||||||||
|
BD Biosciences: FACSAria III Cell Sorter Resource Report Resource Website 100+ mentions |
BD Biosciences: FACSAria III Cell Sorter (RRID:SCR_016695) | instrument resource | Instrument for cell sorting by BD Biosciences where positive air pressure forces sample cell through an optically gel-coupled cuvette . Hydrodynamic focusing guides particles in a single-file stream through the cuvette, where laser light intercepts the stream at the sample interrogation point.Fluorescence activated cell sorting instrument. Flow cytometer as high speed fixed alignment benchtop cell sorter. Enables multicolor analysis of up to 13 fluorescent markers and two scatter parameters at time. | instrument, equipment, USEDit, BD Biosciences, cell, sorter, positive, air, pressure, force, cell, flow | is listed by: USEDit | Commercially available | https://drive.google.com/file/d/14L46Z9kYGpNi6KVjyhP9KmXogSN7q82n/view?usp=drivesdk | Model_Number_FACSAria_III | https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/BD-FACSAria-III-Cell-Sorter-Brochure.pdf, https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/FACSDiva_Software_Brochure.pdf | http://www.bdbiosciences.com/us/instruments/research/cell-sorters/bd-facsaria-iii/m/744763/features | SCR_016695 | BD FACSARIA III cell sorter, BD FACSARIA III | 2026-09-12 12:58:43 | 106 | |||||
|
Appion Package Resource Report Resource Website 10+ mentions |
Appion Package (RRID:SCR_016734) | Appion | data processing software, image analysis software, image processing software, software application, software resource | Software package for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools. | processing, analysis, electron, microscope, image | ARCS ; NCRR RR023093; NCRR RR17573 |
PMID:19263523 | Free, Available for download, Freely available | http://www.appion.org | SCR_016734 | 2026-09-12 12:58:44 | 16 | |||||||
|
dCAS Resource Report Resource Website |
dCAS (RRID:SCR_016612) | dCAS | software resource, web application | Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | automate, large, scale, cDNA, sequence, analysis, BLAST, database, gene | is listed by: NIAID | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016612 | Desktop cDNA Annotation System | 2026-09-12 12:58:42 | 0 |
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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 U24DK097771.
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