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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SequelQC Resource Report Resource Website 1+ mentions |
SequelQC (RRID:SCR_017279) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data. | raw, data, PacBio, Sequel, analysis, sequence, DNA, read, length, plot | NSF Plant Genome Research Program IOS-1744001 | DOI:10.1101/611814 | Free, Freely available, Available for download | SCR_017279 | 2026-08-06 09:29:01 | 2 | |||||||||
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QtiPlot Resource Report Resource Website 10+ mentions |
QtiPlot (RRID:SCR_017311) | data analysis software, software application, software resource, data processing software | Software tool for data analysis and scientific visualization by IONDEV SRL. | data, analysis, visualization, IONDEV SRL | Restricted | SCR_017311 | 2026-08-06 09:29:02 | 28 | |||||||||||
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SCÅTTER Resource Report Resource Website 50+ mentions |
SCÅTTER (RRID:SCR_017271) | software resource, data access protocol, service resource, production service resource, web service, analysis service resource | Software JAVA based application for basic analysis of Small Angle X-ray Scattering datasets. | analysis, data, dataset, small, angle, X ray, scattering, SAXS, BIOISIS | Department of Energy Office of Science Integrated Diffraction Analysis Technologies ; National Cancer Institute Structural Cell Biology of DNA Repair Machines ; National Institute of General Medical Sciences project MINOS |
Restricted | https://bl1231.als.lbl.gov/scatter/ | SCR_017271 | 2026-08-06 09:29:02 | 84 | |||||||||
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The Immunology Database and Analysis Portal (ImmPort) Resource Report Resource Website 500+ mentions |
The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) | ImmPort | storage service resource, ontology, controlled vocabulary, topical portal, service resource, data repository, disease-related portal, data or information resource, portal, database | Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology. | immunology, basic, clinical, data, share, store, analyze, exchange, dataset, immune, mediated, disease, analysis, tool, FASEB list |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NIDDK Research Resources is affiliated with: Cytokine Registry is related to: MetaCyto is related to: The 10000 Immunomes is related to: NIAID |
Immune mediated disease | NIH ; NIAID ; DAIT ; NIAID HHSN266200400076C; NIAID HHSN272201200028C |
PMID:24791905 | nlx_152691, r3d100012529 | http://www.immport.org/immport-open/public/home/home, http://www.immport.org/ | http://www.immport.org | SCR_012804 | Immunology Data and Analysis Portal, ImmPort system, ImmPort, Immunology Database and Analysis Portal | 2026-08-06 09:28:03 | 987 | |||
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HED Tags Resource Report Resource Website 1+ mentions |
HED Tags (RRID:SCR_014074) | HED | standard specification, narrative resource, data or information resource | Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging. | Data, structure, standard, EEG, brain, imaging, comma, separated, path, string, analysis, MEG, fNIRS, multimodal, ECG, EMG, GSR, behavioral, BRAIN Initiative |
is used by: NIMH Data Archive is used by: HeadIT is used by: OpenNeuro is recommended by: BRAIN Initiative has parent organization: University of California at San Diego; California; USA |
Swartz Foundation ; Army Research Laboratory Cooperative Agreement ; NIMH R01MH084819; NINDS R01 NS047293 |
PMID:27799907 | Free, Freely available | SCR_017630 | SCR_014074 | Hierarchical Event Descriptor Tags, Hierarchical Event Descriptor, HED, HED tags | 2026-08-06 09:28:15 | 7 | |||||
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Skyline Resource Report Resource Website 1000+ mentions |
Skyline (RRID:SCR_014080) | data analysis software, software application, software resource, data processing software | Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences. | Proteomics, SRM, MRM, DDA, DIA, shotgun, mass, spectrometry, data, analysis, quantitative |
uses: MSstats is related to: ProteoWizard has parent organization: University of Washington; Seattle; USA works with: PanoramaWeb |
NCI U24 CA126479; NIDDK R01 DK069386; NCRR P41 RR011823; NIA P30 AG013280; NHLBI R01 HL082747 |
PMID:20147306 | Free, Available for download, Freely available | SCR_014080 | 2026-08-06 09:28:15 | 2805 | ||||||||
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Origin Resource Report Resource Website 10000+ mentions |
Origin (RRID:SCR_014212) | software resource, data analysis software, data processing software, data visualization software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing. | data, analysis, software, authoring, tool, scripting, graphing, statistical, publication |
is listed by: SoftCite is related to: OriginPro |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015636 | https://www.originlab.com/index.aspx?go=PRODUCTS&PID=1834 | SCR_014212 | OriginPro | 2026-08-06 09:28:16 | 13956 | |||||||
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FactoMineR Resource Report Resource Website 1000+ mentions |
FactoMineR (RRID:SCR_014602) | data analysis software, software application, software resource, data processing software | Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables. | multivariate, analysis, data, structure, organized, group, variable, individual, hierarchy |
is used by: ClustVis is listed by: CRAN |
https://cran.r-project.org/web/packages/FactoMineR/index.html, https://github.com/husson/FactoMineR | SCR_014602 | factominer | 2026-08-06 09:28:24 | 2349 | |||||||||
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TIDA Resource Report Resource Website 50+ mentions |
TIDA (RRID:SCR_014582) | software application, data acquisition software, software resource, data processing software | A software which is used to acquire physiological data from the HEKA Patch Clamp Amplifiers and HEKA interfaces. | data acquisition, heka, patch clamp, heka interface, physiological, data, acquisition software | Open source, Paired with a commercial product | SCR_014582 | 2026-08-06 09:28:21 | 96 | |||||||||||
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eQTL Visualization Tool Resource Report Resource Website 1+ mentions |
eQTL Visualization Tool (RRID:SCR_013413) | data visualization software, software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics. | experiment, explore, expression, genome, genetic, genetical, cis, computational, data, database, genomic, grafical, interface, linkage, mine, pqtl type, p-value, repository, tissue, tissue type, trans, visualization, visualize | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10222 | SCR_013413 | eQTLexplorer | 2026-08-06 09:28:08 | 1 | |||||||||
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Statistical Analysis System Resource Report Resource Website 5000+ mentions |
Statistical Analysis System (RRID:SCR_008567) | SAS | software application, data analytics software, data management software, software resource | Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS. | Explore, analyze, visualize, data, standardized, management, statistics | is listed by: SoftCite | Restircted | nif-0000-31484 | https://www.sas.com/en_us/software/platform.html, https://www.sas.com/en_us/software/sas9.html | SCR_008567 | Statistical Analysis System, SAS Intelligence Platform, SAS 9.3, SAS 9.4 | 2026-08-06 09:27:15 | 7165 | ||||||
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STATISTICA Resource Report Resource Website 5000+ mentions |
STATISTICA (RRID:SCR_014213) | software application, data analytics software, software resource | Analytics platform with various sub platforms, each with specific performance capabilities for tasks such as data analysis, data management, data visualization, and data mining procedures. | TIBCO, statistical, test, data, mining, |
is listed by: Metabolomics Workbench is listed by: SoftCite |
Commercially available, Free download available | http://statistica.software.informer.com/10.0/, http://statistica.io/products/ | SCR_014213 | Statistica 10, STATISTICS Product Index, Statistica | 2026-08-06 09:28:17 | 7864 | ||||||||
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CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | software application, data analytics software, software resource | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
Doris Duke Charitable Foundation ; Damon Runyon Cancer Research Foundation ; B&J Cardan Oncology Research Fund ; Ludwig Institute for Cancer Research ; NCI U01 CA154969; NIAID U19 AI090019; NCI T32 CA09302; US Department of Defense ; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-08-06 09:28:59 | 1239 | ||||||
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Scrattch.Hicat Resource Report Resource Website 10+ mentions |
Scrattch.Hicat (RRID:SCR_018099) | software application, data analytics software, software resource | Software R package as hierarchical, iterative clustering for analysis of transcriptomics data.Used for single cell RNA-seq analysis for transcriptomic type characterization from Allen Institute. | Hierarchical, iterative clustering, analysis, transcriptomics, data, single cell RNAseq, Allen Institute | has parent organization: Allen Institute | Free, Available for download, Freely available | SCR_018099 | Scrattch Hierarchical, Iterative Clustering for Analysis of Transcriptomics | 2026-08-06 09:29:16 | 31 | |||||||||
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ODDPub Resource Report Resource Website 1+ mentions |
ODDPub (RRID:SCR_018385) | software resource, algorithm resource | Text mining algorithm to screen biomedical publications to find data sharing statements. Algorithm that parses set of publications and detects which publications disseminated Open Data or Open Code together with publication. Tailored towards biomedical literature. | Text mining, biomedical publication screening, data sharing statement detection, open data, open code, publication, data, biomedical literature, Berlin Institute of Health, ASWG | is used by: rtransparent | Free, Available for download, Freely available | SCR_018385 | 2026-08-06 09:29:25 | 5 | ||||||||||
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BVA import/export EEGLAB plugin Resource Report Resource Website 1+ mentions |
BVA import/export EEGLAB plugin (RRID:SCR_016333) | bva-io | software application, software toolkit, software resource | Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software. | interfacing, brain, vision, analyser, data, file, load, save, Matlab, routine, compatible, EEGLAB |
is related to: SourceForge is related to: EEGLAB is related to: MATLAB |
Free, Available for download, Freely available | SCR_016333 | Brain Vision Analyser | 2026-08-06 09:28:48 | 3 | ||||||||
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Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes Resource Report Resource Website 1+ mentions |
Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) | data set, data or information resource | Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients. | molecular, taxonomy, lung, carcinoma, cancer, death, mrna, expression, sequence, data, adenocarcinoma, neuroendocrine, gene, type ii pneumocyte, analysis, metastasis, integration, mrna expression profiling | has parent organization: Broad Institute | Lung cancer | NCI U01 CA84995 | PMID:11707567 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30292 | SCR_003010 | Cancer Genomics Publication | 2026-08-06 09:25:46 | 2 | |||||
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EyeBrowse Resource Report Resource Website 1+ mentions |
EyeBrowse (RRID:SCR_008000) | data set, data or information resource |
EyeBrowse displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAT search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. For mouse, there is custom track data for ChIP-on-Chip of RNA-Polymerase-II during photoreceptor maturation. |
est, expressed sequence tag, eye, gene, genome, cataract, cdna, chicken, clone, cluster, cornea, cornea disease, cow, data, disease, dog, human, locus, maturation, mouse, myopia, photoreceptor, rat, retina, rhesus, rna polymerase-ii, tag, zebrafish, data analysis software, eye tracking device |
is listed by: 3DVC has parent organization: University of California at Santa Cruz; California; USA |
Retinal disease, Cataract, Myopia, Cornea disease | NEIBank | nif-0000-07733 | SCR_008000 | EyeBrowse | 2026-08-06 09:27:03 | 3 | |||||||
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Dartmouth-Hitchcock Bioinformatics Shared Resource Resource Report Resource Website |
Dartmouth-Hitchcock Bioinformatics Shared Resource (RRID:SCR_009758) | service resource, core facility, access service resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 29,2022. Core to support the implementation of bioinformatics resources for cancer research at Dartmouth. Provides consultation and collaboration for research projects of NCCC members, regular workshops, seminars, services including applied bioinformatics and data mining, computer programming and software engineering, database development and programming and high performance computing and systems administration. | cancer, research, core, service, bioinformatics, data, mining, computer, programming, software, engineering, database, administration |
is listed by: Eagle I has parent organization: Dartmouth College; New Hampshire; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156219 | http://cancer.dartmouth.edu/res/bioinformatics.html | http://dartmouth.eagle-i.net/i/0000012b-3a21-22b4-bd3e-55f580000000 | SCR_009758 | Center, Dartmouth, Norris Cotton, Hitchcock, Dartmouth-Hitchcock, Shared Resource, BISR, Bioinformatics, Cancer | 2026-08-06 09:27:21 | 0 | ||||||
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Howard University Center for Computational Biology and Bioinformatics Core Facility Resource Report Resource Website |
Howard University Center for Computational Biology and Bioinformatics Core Facility (RRID:SCR_009864) | Howard CCBB, CCBB | core facility, service resource, access service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core for bioinformatics consultation and software access. Laboratory of Molecular Computations and Bioinformatics (LMCB) is a resource facility dedicated to the support of computational biomedical research at Howard University. Provides molecular modeling, molecular dynamics, bioinformatics, and computational quantum chemistry capabilities and support to a variety of research projects at Howard University. | data, analysis, bioinformatics, software, access, consultation, molecular, computation, biomedical, quantum, chemistry |
is listed by: Eagle I has parent organization: Howard University; Washington D.C. |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156335 | https://rcmi.howard.edu/ccbb-3/ | http://www.howard.edu/medicine/rcmi/LMCB/default.htm | SCR_009864 | , LMCB, Laboratory of Molecular Computations and Bioinformatics, Howard, CCBB | 2026-08-06 09:27:23 | 0 |
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