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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Best Apnea Interventions for Research (BestAIR) sleep study Resource Report Resource Website 1+ mentions |
Best Apnea Interventions for Research (BestAIR) sleep study (RRID:SCR_016583) | BestAIR | data or information resource, disease-related portal, portal, topical portal | Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume. | data, analysis, sleep, apnea, treatment, cardiovascular, disease, risk, factor, polysomnography, ECG, SpO2 | is listed by: National Sleep Research Resource (NSRR) | sleep apnea, cardiovascular disease | NHLBI U34 HL105277; Philips Respironics ; ResMed Foundation |
DOI:10.5665/sleep.4266 | SCR_016583 | bestair, , Best Apnea Interventions for Research, Bestair | 2026-09-05 06:28:11 | 3 | ||||||
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riboWaltz Resource Report Resource Website 10+ mentions |
riboWaltz (RRID:SCR_016948) | data analysis software, data processing software, data visualization software, software application, 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 | 2026-09-05 06:28:16 | 23 | ||||||||
|
TopDom Resource Report Resource Website 10+ mentions |
TopDom (RRID:SCR_016964) | TOPDOM | data analysis software, data processing software, software application, software resource, software toolkit | 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 |
Arnold and Mabel Beckman foundation ; NHLBI U01 HL108634; NIDDK U54 DK107981; NSF CAREER 0747475; NSF CAREER 1150287; 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 | 2026-09-05 06:28:16 | 11 | ||||||
|
NZYTech Resource Report Resource Website 10+ mentions |
NZYTech (RRID:SCR_016772) | organization | Commercially provides services and products for research in the fields of molecular biology, diagnostics, enzymes and proteins. | biomaterial, analysis, service, production, supplier, molecular, biology, diagnostics, enzyme, protein | grid.436825.e, Wikidata: Q30291029 | https://ror.org/00rtryt44 | SCR_016772 | Lda. � Genes and Enzymes, NZYTech | 2026-09-05 06:28:14 | 13 | |||||||||
|
smMIPfil Resource Report Resource Website 1+ mentions |
smMIPfil (RRID:SCR_016892) | data analysis software, data processing software, software application, software resource | Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required. | nucleotide, DNA, read, unique, molecular, identifier, single, inversion, probe, data, analysis, mutation, sequence | requires: SAMTOOLS | Free, Available for download, Freely available | SCR_016892 | single molecule Molecular Inversion Probesfil, smMIPfil | 2026-09-05 06:28:15 | 2 | |||||||||
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Thunder STORM Resource Report Resource Website 10+ mentions |
Thunder STORM (RRID:SCR_016897) | ThunderSTORM | data analysis software, data processing software, software application, software resource, software toolkit | 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 |
Charles University ; Czech Science Foundation ; European Regional Development Fund ; European Social Fund |
PMID:24771516 | Free, Available for download, Freely available | biotools:thunderstorm | https://bio.tools/thunderstorm | SCR_016897 | 2026-09-05 06:28:15 | 48 | |||||
|
CRISPR-P Resource Report Resource Website 10+ mentions |
CRISPR-P (RRID:SCR_016941) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment. | synthetic, single, RNA, CRISP, plant, Cas9, target, DNA, sequence, analysis, restriction, enzyme, sgRNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
Fundamental Research Funds for the Central Universities ; National Basic Research Program of China ; Program for New Century Excellent Talents in University |
PMID:24719468 | Free, Freely available | biotools:CRISPR-P | https://bio.tools/CRISPR-P | SCR_016941 | CRISPR-P 2.0, Clustered Regularly Interspaced Short Palindromic Repeats P, CRISPR P | 2026-09-05 06:28:15 | 42 | |||||
|
ascat Resource Report Resource Website 10+ mentions |
ascat (RRID:SCR_016868) | ASCAT | data analysis software, data processing software, software application, software resource | Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data. | allele, specific, copy, number, analysis, tumor, purity, ploidy, sequencing, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:20837533 | Free, Available for download, Freely available | BioTools:ascat, biotools:ascat | https://github.com/VanLoo-lab/ascat, https://www.crick.ac.uk/research/labs/peter-van-loo/software, https://bio.tools/ascat, https://sources.debian.org/src/r-other-ascat/ | SCR_016868 | ASCAT 3.0, ASCAT 2.0, ASCAT 4.0, ASCAT 1.0, Allele-Specific Copy Number Analysis of Tumors, Allele Specific Copy Number Analysis of Tumors | 2026-09-05 06:28:14 | 42 | |||||
|
Pyclone Resource Report Resource Website 10+ mentions |
Pyclone (RRID:SCR_016873) | data analysis software, data processing software, software application, software resource | Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing. | infer, prevalence, point, mutation, heterogeneous, cancer, probabilistic, population, NGS, sequencing, data, analysis | PMID:24633410 | Available for download, Free for academic, nonprofit use | https://bitbucket.org/aroth85/pyclone/wiki/Home | SCR_016873 | PyClone | 2026-09-05 06:28:14 | 46 | ||||||||
|
Metab Resource Report Resource Website 1+ mentions |
Metab (RRID:SCR_016877) | Metab | data analysis software, data processing software, software application, software resource, software toolkit | 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 | 2026-09-05 06:28:15 | 1 | ||||||
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OpenBMI Resource Report Resource Website 1+ mentions |
OpenBMI (RRID:SCR_016876) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | 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 | 2026-09-05 06:28:14 | 5 | |||||||||
|
BioNano: Irys system Resource Report Resource Website 10+ mentions |
BioNano: Irys system (RRID:SCR_016754) | instrument resource | System by BioNano Genomics ( formerly BioNanomatrix) which provides optical next generation mapping (NGM). Used for sequence assembly and structural variation analysis. Provides Scaffold Bionano genome mapping data with sequencing data to improve assembly contiguity, reduce sequencing coverage needed, and automatically correct errors in sequencing based assemblies. | instrument, Irys, system, BioNano Genomics, BioNanomatrix, optical, next, generation, mapping, sequence, assembly, structural, variation, analysis, data, | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_016754.pdf | https://bionanogenomics.com/wp-content/uploads/2017/01/2016-Irys-System-Brochure.pdf | https://bionanogenomics.com/technology/genome-assembly/ | SCR_016754 | 2026-09-05 06:28:13 | 35 | ||||||||
|
Phenograph Resource Report Resource Website 100+ mentions |
Phenograph (RRID:SCR_016919) | PhenoGraph | data analysis software, data processing software, software application, software resource | Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity. | high, dimention, single, cell, data, phenotype, analysis, heterogeneity |
uses: Python Programming Language is related to: Rphenograph |
CIRM DR1 01477; CIRM RB201592; Entertainment Industry Foundation ; NCI P01 CA034233; NCI R01 CA130826; NCI R01 CA164729; NCI U54 CA121852; NCI U54 CA143907; NCI U54 CA149145; NIAID U19 AI057229; NICHD DP1 HD084071; NIGMS R00 GM104148; NIH Office of the Director DP2 OD002414; NIH N01 HV00242; Packard Fellowship for Science and Engineering ; Rachford and Carlota Harris Endowed Professorship ; Stand Up To Cancer Phillip A. Sharp Award SU2CAACRPS04; US Department of Health and Human Services HHSN272200700038C; US DOD W81XWH1210591; US FDA HHSF223201210194C |
PMID:26095251 | Free, Available for download, Freely available | https://github.com/JinmiaoChenLab/Rphenograph | https://github.com/jacoblevine/PhenoGraph | SCR_016919 | 2026-09-05 06:28:15 | 235 | |||||
|
clusterProfiler Resource Report Resource Website 10000+ mentions |
clusterProfiler (RRID:SCR_016884) | data analysis software, data processing software, data visualization software, software application, 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 |
2007 Chang-Jiang Scholars Program ; Fundamental Research Funds for the Central Universities ; Guangdong Natural Science Research Grant ; National 973 Projects of China ; National Natural Science Foundation of China |
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 | 2026-09-05 06:28:15 | 13465 | |||||
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Signal Resource Report Resource Website 10+ mentions |
Signal (RRID:SCR_017081) | data acquisition software, data analysis software, data processing software, software application, software resource | Software package for sweep based data acquisition and analysis of time based waveform data obtained through CED digital analogue converter by Cambridge Electronic Design System Limited. Used for transient capture, patch and voltage clamp, LTP studies, evoked response and TMS. | sweep, based, data, acquisition, analysis, time, based, waveform, data, CED, transient, capture, patch, voltage, clamp, LTP study, evoked, response | Available for purchase | SCR_017081 | Signal Version 6, CED Signal, Cambridge Electronic Design Signal | 2026-09-05 06:28:18 | 13 | ||||||||||
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rCASC Resource Report Resource Website 1+ mentions |
rCASC (RRID:SCR_017005) | data analysis software, data processing software, software application, software resource | Software package for reproducible classification analysis of single cell sequencing data. | reproducibility, classification, analysis, single, cell, sequencing, data, bio.tools |
is used by: Stardust is listed by: Debian is listed by: bio.tools is related to: University of Turin;Turin;Italy |
PMID:24204232 | Free, Available for download, Freely available | biotools:rCASC | https://kendomaniac.github.io/rCASC/, https://bio.tools/rCASC | SCR_017005 | rCASC, reproducible Cluster Analysis of Single Cells | 2026-09-05 06:28:17 | 1 | ||||||
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ImmuneDB Resource Report Resource Website 1+ mentions |
ImmuneDB (RRID:SCR_017125) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features. | collect, store, analysis, B cell, T cell, immune, receptor, sequencing, data, process, raw, read | is used by: AIRR Data Commons | NCI P30 CA016520; NIAID P01 AI106697; NIAID P30 AI0450080; NIDDK UC4 DK112217 |
PMID:30298069 | Free, Available for download, Freely available | https://github.com/arosenfeld/immunedb | SCR_017125 | 2026-09-05 06:28:19 | 8 | |||||||
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Scikit-Criteria Resource Report Resource Website |
Scikit-Criteria (RRID:SCR_017084) | software library, software resource, software toolkit | Software tool as collection of Multiple Criteria Decision Analysis methods integrated into scientific Python stack. | collection, multiple, criteria, decision, analysis, method, integrated, stack | is related to: Python Programming Language | Free, Available for download, Freely available | https://github.com/leliel12/scikit-criteria/blob/master/doc/source/index.rst, https://github.com/leliel12/scikit-criteria, | SCR_017084 | 2026-09-05 06:28:18 | 0 | |||||||||
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SwiftOrtho Resource Report Resource Website 1+ mentions |
SwiftOrtho (RRID:SCR_017122) | data analysis software, data processing software, software application, software resource | Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets. | orthology, analysis, identify, ortholog, paralog, co ortholog, genome, homology, different, species, large, dataset, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/543223 | Free, Available for download, Freely available | OMICS_30890, biotools:SwiftOrtho | https://bio.tools/SwiftOrtho | SCR_017122 | 2026-09-05 06:28:19 | 4 | |||||||
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Haystack Resource Report Resource Website 1+ mentions |
Haystack (RRID:SCR_017087) | data analysis software, data processing software, software application, software resource, software toolkit | Software suite of computational tools implemented in Python to study epigenetic variability, cross cell type plasticity of chromatin states and transcription factors motifs providing mechanistic insights into chromatin structure, cellular identity and gene regulation. Epigenetic variability and transcription factor motifs analysis pipeline. | epigenetic, variability, cell, plasticity, chromatin, transcription, factor, motif, structure, gene, regulation, analysis |
is related to: Python Programming Language has parent organization: Harvard University; Cambridge; Massachusetts |
Free, Available for download, Freely available | https://github.com/pinellolab/haystack_bio | SCR_017087 | haystack, haystack_bio | 2026-09-05 06:28:18 | 3 |
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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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