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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Sniffles Resource Report Resource Website 50+ mentions |
Sniffles (RRID:SCR_017619) | software resource, software application, data processing software | Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates. | Structural, variation, caller, third, generation, sequencing, SV, split, read, alignment, mismatch, region, analysis, error, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:sniffles | https://bio.tools/sniffles | SCR_017619 | 2026-08-08 12:03:24 | 76 | ||||||
|
Broad Terra cloud commons for pathogen surveillance Resource Report Resource Website 10+ mentions |
Broad Terra cloud commons for pathogen surveillance (RRID:SCR_018278) | data or information resource, portal | Broad Terra cloud workspace for best practices with COVID-19 genomics data. Raw COVID-19 sequencing data from NCBI Sequence Read Archive. Workflows for genome assembly, quality control, metagenomic classification, and aggregate statistics. | COVID-19, COVID-19 data, analysis, collaborate, genomic data, sequencing data, NCBI SRA, genome assembly workflow, quality control, metagenomic classification |
is listed by: Data and Computational Resources to Address COVID-19 is listed by: Terra has parent organization: Broad Institute |
COVID-19 | Free, Freely available | SCR_018278 | Terra | 2026-08-08 12:03:24 | 39 | ||||||||
|
Image Quant TL Resource Report Resource Website 100+ mentions |
Image Quant TL (RRID:SCR_018374) | software resource, software application, image analysis software, data processing software | Software tool for image analysis by Cytiva. Automated image analysis software for general purpose electrophoresis gel, blot, arrays and colony counting. | Image analysis, Cytiva, image, electrophoresis gel image, blot image, array, colony count image, analysis | SCR_018374 | , Image Quant TL array analysis, ImageQuant TL 8.2 | 2026-08-08 12:03:24 | 381 | |||||||||||
|
Stereo Investigator - Whole Slide Edition Resource Report Resource Website 1+ mentions |
Stereo Investigator - Whole Slide Edition (RRID:SCR_017667) | software resource, software application, image analysis software, data processing software | Software tool for quantitative analysis using stereology on whole slide images. Used to analyze whole slide image data. Includes number, length, area and volume analyses. | Quantitative, analysis, stereology, whole, slide, image, MBF Bioscience | Restricted | SCR_017667 | 2026-08-08 12:03:23 | 3 | |||||||||||
|
HALO Resource Report Resource Website 100+ mentions |
HALO (RRID:SCR_018350) | HALO | software resource, software application, image analysis software, data processing software | Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology. | Image analysis platform, digital pathology, quantitative tissue analysis, image, analysis, tissue | is listed by: SoftCite | Restricted | SCR_018350 | Indica Labs HALO software | 2026-08-08 12:03:24 | 108 | ||||||||
|
Harmony Resource Report Resource Website 10+ mentions |
Harmony (RRID:SCR_018809) | image acquisition software, image analysis software, data acquisition software, software resource, software application, data processing software | Harmony high content imaging and analysis software. Used to quantify complex cellular phenotypes. Designed for PerkinElmer high content screening systems. | Imaging, analysis, cellular phenotype quantification, PerkinElmer, high content, screening system, cell phenotypic screening, live cell imaging, | is related to: Perkin Elmer: Operetta CLS | Restricted | SCR_018809 | Harmony 4.8 | 2026-08-08 12:01:23 | 34 | |||||||||
|
RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | software resource, software application, data analysis software, data processing software | Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data. | Ribo-seq data, analysis, ribosome profiling experiment, triplet periodicity, ribosomal footprint, translated region, three nucleotide periodicity, data, ribosome profiling, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIGMS R01 GM104962; Berlin Institute for Medical Systems Biology |
PMID:26657557 | Free, Freely available | biotools:ribotaper | https://bioconda.github.io/recipes/ribotaper/README.html, https://bio.tools/ribotaper | SCR_018880 | 2026-08-08 12:01:16 | 8 | ||||||
|
IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | software resource, software application, data analysis software, data processing software | Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences. | T cell receptor, antibody, immunoglobulin, immunoinformatics, next generation sequencing, statistical significance, clonotype diversity, clonotype expression, pairwise comparison, gene, NGS, analysis, antybody clonotype, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:27667992 | Free, Available for download, Freely available | biotools:IMGt_StatClonotype | https://bio.tools/IMGT_StatClonotype | SCR_018963 | IMGTStatClonotype, ImMunoGeneTics/StatClonotype | 2026-08-08 12:01:25 | 4 | ||||||
|
ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | software resource, software application, data analysis software, data visualization software, data processing software | Software Python package for analysis of trajectories in clinical datasets. | Trajectories analysis, clinical datasets, analysis, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:clintrajan | https://bio.tools/clintrajan | SCR_019018 | 2026-08-08 12:01:26 | 1 | ||||||||
|
TwoSampleMR Resource Report Resource Website 500+ mentions |
TwoSampleMR (RRID:SCR_019010) | software resource, software application, data analysis software, data processing software | Software R package for performing Mendelian randomization using genome wide association study summary data. | GWAS data, genome wide associated study data, genome data, Mendelian randomization, analysis | PMID:29846171 | Free, Available for download, Freely available | SCR_019010 | 2026-08-08 12:01:19 | 732 | ||||||||||
|
CoVIC-DB Database Resource Report Resource Website 1+ mentions |
CoVIC-DB Database (RRID:SCR_018339) | CoVIC-DB | database, data or information resource, catalog | Serves as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. Most potent antibodies will guide development of vaccines to stop current outbreak and protect against future pandemics. | SARS-CoV-2, monoclonal antibodies, antibody, antibody contribution, analysis, antibody based immunotherapy, COVID-19, COVID-19 data | is related to: Coronavirus Immunotherapy Consortium | COVID-19 | Bill and Melinda Gates Foundation ; Wellcome and MasterCard Impact Fund |
Free, Freely available | SCR_018339 | Coronavirus Immunotherapy Consortium Database | 2026-08-08 12:02:43 | 2 | ||||||
|
REDCap Resource Report Resource Website 10000+ mentions |
REDCap (RRID:SCR_003445) | REDCap | web application, software resource | Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions. | online survey, survey, database, translational research, informatics, workflow, clinical research, clinical, metadata, biomedical, online form, data capture, management, analysis, data sharing, data collection, data standard, best practice, data collection instrument, electronic data capture |
is listed by: Biositemaps is listed by: SoftCite is related to: Clinical and Translational Science Awards Consortium has parent organization: Vanderbilt University; Tennessee; USA works with: redcap-completion works with: aux-file-upload |
NIH ; UL1 RR029882 ; UL1 TR000062 ; UL1 RR026314 ; UL1 TR000077 ; UL1 RR024975 ; UL1 TR000445 ; G12 RR003051 ; G12 MD007600 ; UL1 RR024150 ; UL1 TR000135 ; R24 HD042849 ; UL1 RR024989 ; UL1 TR000439 |
PMID:23149159 PMID:18929686 |
Software is available at no cost for REDCap Consortium Partners. If not in the consortium, See the Become a Partner page to find more information about joining our group. | nif-0000-33254 | SCR_003445 | RED Cap, Research Electronic Data Capture, The REDCap Consortium | 2026-08-08 12:02:42 | 23733 | |||||
|
SBIA Resource Report Resource Website 1+ mentions |
SBIA (RRID:SCR_013628) | SBIA | access service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. A section of the Penn department of radiology, it is devoted to the development of computer-based image analysis methods and their application to clinical research studies. Image analysis methodologies include image registration, segmentation, population-based statistical analysis, biophysical modeling of anatomical deformations, and high-dimensional pattern classification. Clinical research studies spans a variety of clinical areas and organs, and they include brain diseases such as Alzheimer's disease and schizophrenia, evaluation of treatment effects in large clinical trials, diagnosis of cardiac diseases, and diagnosis prostate, breast and brain cancer. SBIA also performs small animal imaging research aiming to understand brain development in mouse models. It has multiple resources which can be accessed by researcher. | effect, alzheimer's, analysis, anatomical, biomedical, biophysical, brain, cancer, breast cancer, cardiac, classification, clinical, computer, deformation, dimensional, disease, method, model, mouse, organ, pattern, prostate, registration, schizophrenia, segmentation, statistical analysis, study, treatment, image | has parent organization: University of Pennsylvania; Philadelphia; USA | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-33052 | SCR_013628 | The Section for Biomedical Image Analysis, Section for Biomedical Image Analysis | 2026-08-08 12:02:53 | 4 | |||||||
|
TREES toolbox Resource Report Resource Website 10+ mentions |
TREES toolbox (RRID:SCR_010457) | TREES toolbox | software resource | Software package, written in Matlab (Mathworks, Natick, MA), providing tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees. It provides the basic tools to edit, visualize and analyze dendritic and axonal trees, methods for quantitatively comparing branching structures between neurons, and tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distance. | neuronal branching, microscopy, neuron, matlab, visualization, rendering, reconstruction, analysis, modeling, morphology, dendrite, axon, computational neuroanatomy, tree |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
Max Planck Society ; Wellcome Trust ; Gatsby Charitable Foundation ; Alexander von Humboldt-Stiftung ; European Research Council |
PMID:20700495 | GNU General Public License v3, Creative Commons Attribution-NonCommercial-ShareAlike License v3, The community can contribute to this resource | nlx_157723 | http://www.nitrc.org/projects/treestoolbox | SCR_010457 | treestoolbox - A Matlab toolbox to generate edit visualize and analyze neuronal structure | 2026-08-08 11:59:31 | 29 | ||||
|
miRDeep Resource Report Resource Website 100+ mentions |
miRDeep (RRID:SCR_010829) | miRDeep2 | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data. | miRNA, gene, animal, clade, analysis, sequence, RNA, data | is listed by: OMICtools | Helmholtz-Alliance on Systems Biology ; Helmholtz Association ; German Ministry of Education and Research ; Senate of Berlin ; China Scholarship Council ; Max Delbrück Centrum Systems Biology Network |
PMID:18392026 PMID:21911355 |
Free, Available for download, Freely available | OMICS_00373 | https://github.com/rajewsky-lab/mirdeep2 | SCR_010829 | 2026-08-08 11:59:37 | 182 | |||||
|
PSIPRED Resource Report Resource Website 1000+ mentions |
PSIPRED (RRID:SCR_010246) | production service resource, web service, software resource, data access protocol, analysis service resource, service resource | Web tool as secondary structure prediction method, incorporating two feed forward neural networks which perform analysis on output obtained from PSI-BLAST. Web server offering analyses of protein sequences. | Predict Secondary Structure, protein analysis, secondary structure prediction, protein sequence, sequence analysis, protein, analysis |
is listed by: Debian is listed by: SoftCite has parent organization: University College London; London; United Kingdom |
Biotechnology and Biological Science Research Council ; University College London |
DOI:10.1093/nar/gkz297 | Free, Freely available | SCR_018546, nlx_156884 | https://sources.debian.org/src/psipred/ | SCR_010246 | PSIPRED Protein Sequence Analysis Workbench, PSIPRED 4.0 | 2026-08-08 11:59:25 | 1935 | |||||
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Illumina Resource Report Resource Website 1000+ mentions |
Illumina (RRID:SCR_010233) | Illumina, Inc. | commercial organization | American company incorporated that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Provides a line of products and services that serve the sequencing, genotyping and gene expression and proteomics markets. Its headquarters are located in San Diego, California. | Commercial, organization, develope, manufacture, system, analysis, genetic, sequencing, genotyping, gene, expression, proteomic |
is related to: fermi-lite is related to: Illumina: NextSeq 2000 system is parent organization of: Strelka2 is parent organization of: Tk-GO is parent organization of: BaseSpace is parent organization of: Illumina: iSeq 100 Sequencing System |
nlx_156846, grid.185669.5, Wikidata: Q2068984, ISNI: 0000 0004 0507 3954 | https://ror.org/05k34t975 | SCR_010233 | Inc., Illumina | 2026-08-08 11:59:17 | 2543 | |||||||
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TMA Navigator Resource Report Resource Website 1+ mentions |
TMA Navigator (RRID:SCR_005599) | TMA Navigator | analysis service resource, data analysis service, production service resource, service resource | A free web-based service open to all users for analysis of tissue microarray (TMA) data and related information, accommodating categorical, semi-continuous and continuous expression scores. There is no login requirement. | tissue microarray, network, analysis, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23761446 | Acknowledgement requested, Free | biotools:tma_navigator, OMICS_00821 | https://bio.tools/tma_navigator | SCR_005599 | 2026-08-08 12:04:04 | 5 | ||||||
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GraphWeb Resource Report Resource Website 10+ mentions |
GraphWeb (RRID:SCR_005746) | GraphWeb | analysis service resource, data analysis service, production service resource, service resource | GraphWeb allows the detection of modules from biological, heterogeneous and multi-species networks, and the interpretation of detected modules using Gene Ontology, cis-regulatory motifs and biological pathways. GraphWeb is a public web server for graph-based analysis of biological networks that: * analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes; * integrates multiple diverse datasets into global networks; * incorporates multispecies data using gene orthology mapping; * filters nodes and edges based on dataset support, edge weight and node annotation; * detects gene modules from networks using a collection of algorithms; * interprets discovered modules using Gene Ontology, pathways, and cis-regulatory motifs. Platform: Online tool | analysis, biological network, ontology or annotation visualization, protein interaction, gene id conversion, orthology mapping, network visualization, graph clustering, gene ontology, cis-regulatory motif, module, network, pathway, biological pathway, motif, visualization, protein interaction, orthology mapping, network visualization, graph clustering, analysis, statistical analysis, term enrichment |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: BIIT - Bioinformatics Algorithmics and Data Mining Group |
European Union FP6 ENFIN LSHG-CT-2005-518254; European Union FP6 COBRED LSHB-CT-2007-037730; Estonian Science Foundation ETF7437 |
PMID:18460544 | Open unspecified license - Free for academic use | nlx_149205 | SCR_005746 | 2026-08-08 12:04:05 | 12 | ||||||
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CateGOrizer Resource Report Resource Website 50+ mentions |
CateGOrizer (RRID:SCR_005737) | CateGOrizer | analysis service resource, data analysis service, production service resource, service resource | CateGOrizer takes batch input of GO term IDs in a list format or unformatted plain text file, allows users to choose one of the available classifications such as GO_slim, GOA, EGAD, MGI_GO_slim, GO-ROOT, or a self-defined classification list, find its parental branch and performs an accumulative classification count, and returns the results in a sorted table of counts, percentages, and a pie chart (if it takes longer than standard time out period, it will email the user with a URL link to the results). This tool is comprised with a set of perl CGI programs coupled with a MySQL DBMS that stores the GO terms DAG data. Platform: Online tool | gene ontology, statistical analysis, slimmer-type tool, go term classification, classification, analysis, go slim |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: NAGRP Bioinformatics Coordination Program |
Free for academic use | nlx_149197 | SCR_005737 | GO Terms Classifications Counter | 2026-08-08 12:03:54 | 85 |
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