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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-03 04:54:09 | 13 | ||||||||||
|
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 | 2026-09-03 04:54:14 | 1 | ||||||
|
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 | 2026-09-03 04:54:26 | 0 | |||||||||
|
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 | 2026-09-03 04:54:06 | 3 | ||||||||
|
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 | 2026-09-03 04:54:10 | 11 | ||||||
|
Experimental Design Assistant Resource Report Resource Website 100+ mentions |
Experimental Design Assistant (RRID:SCR_017019) | EDA | service resource, software resource, web application | Web based tool to help in vivo researchers improve design, conduct, analysis and reporting of animal experiments.Provides automated feedback on proposed design and generates graphical summary that aids communication with colleagues, founders and regulatory authorities. Addresses causes of irreproducibility. | in vivo, design, conduct, analysis, reporting, animal, experiment, irreproducibility, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NC3Rs |
PMID:28957312 | Free, Freely available | biotools:eda | https://bio.tools/eda | SCR_017019 | EDA, Experimental Design Assistant (EDA), Experimental Design Assistant | 2026-09-03 04:54:12 | 192 | |||||
|
LION/web Resource Report Resource Website 10+ mentions |
LION/web (RRID:SCR_017018) | Lipid Ontology (LION) | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | Web based ontology enrichment tool for lipidomic data analysis. Used for lipidomics to search for enriched LION-terms in lipidomic subsets. LION-terms contain detailed lipid classification by LIPIDMAPS, biophysical data, lipid functions and organelle associations. Freely accessible in a platform independent way. | lipid, ontology, enrichment, lipidomic, data, analysis, biophysical | is related to: Utrecht University; Utrecht; Netherlands | DOI:10.1101/398040 | Free, Freely available | SCR_017018 | The Lipid Ontology (LION), Lipid Ontology, LIpid ONtology (LION), LIpid ONtology, LION | 2026-09-03 04:54:22 | 33 | |||||||
|
Anima Resource Report Resource Website 10+ mentions |
Anima (RRID:SCR_017017) | 3d spatial image, data analysis software, data or information resource, data processing software, diffusion-weighted mri 3d image, image, image analysis software, image processing software, mri 3d image, portal, registration software, software application, software resource, software toolkit | Portal provides software library and python scripts for medical image processing. Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS including OSX, Fedora, Ubuntu, Windows. | medical, image, processing, analysis, registration, statistical, quantitative, MRI, data, VISAGES |
is related to: Anima scripts is related to: Empenn has parent organization: VISAGES Research |
Free, Freely available, Available for download | http://olivier.commowick.org/software_anima.php | SCR_017017 | 2026-09-03 04:54:02 | 20 | |||||||||
|
GAGE Resource Report Resource Website 50+ mentions |
GAGE (RRID:SCR_017067) | data analysis software, data processing software, software application, software resource | Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies. | gene, set, enrichment, pathway, batch, comparison, parallel, analysis, heterogeneous, data |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017067 | Generally Applicable Gene-set Enrichment for pathway analysis, gage, Generally Applicable Gene-set Enrichment, GSEA | 2026-09-03 04:54:18 | 53 | |||||||||
|
Empenn Resource Report Resource Website |
Empenn (RRID:SCR_017074) | community building portal, data or information resource, disease-related portal, portal, project portal, topical portal | Project between Inria, Inserm, CNRS, and University of Rennes for biomedical image analysis for understanding neurological disease. Used to diagnose, monitor and deliver treatment for mental, neurological and substance use disorders by establishing multidisciplinary team between information sciences and medicine in medical imaging, neuroinformatics and population cohorts. | biomedical, image, analysis, disease, medical, imaging, neuroinformatics, population, cohort, brain, neurological, disorder |
is related to: Anima scripts is related to: VISAGES Research is related to: University of Rennes 1; Rennes; France is related to: Anima |
SCR_017074 | Brain | 2026-09-03 04:54:19 | 0 | ||||||||||
|
Source code for analysis of GC-MS data - Rice HxD Project Resource Report Resource Website 1+ mentions |
Source code for analysis of GC-MS data - Rice HxD Project (RRID:SCR_017073) | data analysis software, data processing software, data visualization software, software application, software resource, source code | Source code used in the analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice exposed to combined drought and heat stress. | analysis, GC-MS, data, rice, sample, statistics, workflow | Free, Available for download, Freely available | SCR_017073 | 2026-09-03 04:54:13 | 1 | |||||||||||
|
Anima scripts Resource Report Resource Website 10+ mentions |
Anima scripts (RRID:SCR_017072) | data processing software, image processing software, software application, software resource | Open source scripts for medical image processing. Provides set of scripts in Python shell. These scripts use essentially tools from Anima to perform more complex series like image preprocessing, model estimation, atlas creation. | medical, image, processing, analysis, registration, atlas, diffusion, MRI |
is related to: Anima is related to: Empenn is related to: Python Programming Language has parent organization: VISAGES Research |
Free, Available for download, Freely available | https://anima.irisa.fr | SCR_017072 | 2026-09-03 04:54:15 | 14 | |||||||||
|
VORTEX Resource Report Resource Website 10+ mentions |
VORTEX (RRID:SCR_017047) | data analysis software, data processing software, software application, software resource | Software Java graphical tool for single cell analysis, clustering and visualization. Provides multithreaded implementations of clustering algorithms, including nonparametric density based X shift, Hierarchical clustering, Mean shift and K medoids. | single, cell, analysis, clustering, visualization, nonparametric, density, based, X shift | has parent organization: Stanford University; Stanford; California | PMID:27183440 | Free, Available for download, Freely available | http://web.stanford.edu/~samusik/vortex/ | SCR_017047 | VorteX Clustering Environment | 2026-09-03 04:54:24 | 19 | |||||||
|
HaTSPiL Resource Report Resource Website 1+ mentions |
HaTSPiL (RRID:SCR_017059) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software Python tool for high throughput sequencing analysis, focused on high reliability, modularity and customisability. | next, generation, sequencing, pipeline, metadata, analysis, mutation, barcoding, customisability, modularity, bio.tools |
uses: Python Programming Language is listed by: Debian is listed by: bio.tools has parent organization: Italian Institute for Genomic Medicine; Turin; Italy |
Free, Available for download, Freely available | biotools:HatSPiL | https://bio.tools/HaTSPiL | SCR_017059 | 2026-09-03 04:54:14 | 1 | ||||||||
|
COsleep Resource Report Resource Website 1+ mentions |
COsleep (RRID:SCR_017053) | cosleep | data analysis software, data processing software, software application, software resource | Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton. | SpiSOP, OpenBCI, sleep, EEG, analysis, electroencephalogram, electrical, activity, brain, wave, pattern, disorder |
is related to: SpiSOP is related to: Python Programming Language |
Free, Available for download, Freely available | http://www.spisop.org/cosleep | SCR_017053 | Closed- and Open-loop Sleep Stimulations with Auditory Stimuli, Closed and Open loop sleep | 2026-09-03 04:54:12 | 1 | |||||||
|
affydata Resource Report Resource Website |
affydata (RRID:SCR_016976) | AffyData | data analysis software, data or information resource, data processing software, software application, software resource | Software R package for analysis of Affymetrix Data. Contains samples data files of a large size. | analysis, Affymetrix, data, large, dataset, oligonucleotide, array |
is listed by: Bioconductor is related to: affy is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016976 | affydata, Affymetrix Data, Affymetrix Data for Demonstration Purpose | 2026-09-03 04:54:04 | 0 | ||||||||
|
CCPN Analysis Resource Report Resource Website 10+ mentions |
CCPN Analysis (RRID:SCR_016984) | CcpNmr Analysis | data analysis software, data processing software, data visualization software, software application, software resource | Software package for interactive NMR spectrum visualization, resonance assignment and data analysis. Graphical elements allow to enter information and to view status of data and library functions manipulate the CCPN data model objects to record the scientific information. Software is cross platform and works on Linux, Mac OSX, Windows and Unix. | interactive, NMR, specturm, visualization, resonance, data, analysis |
is related to: University of Cambridge; Cambridge; United Kingdom is related to: Python Programming Language is related to: Collaborative Computing Project for NMR works with: CCPN Data Model works with: CCPN Data Model |
Biotechnology and Biological Sciences Research Council (UK) ; Deutsche Forschungsgemeinschaft |
PMID:21953355 PMID:15815974 |
Public, Available for download, Free of charge for non profit institutions, Tutorial available | SCR_016984 | CcpNmr Analysis, CCPN Analysis v2, CCPN Analysis v3 | 2026-09-03 04:54:09 | 48 | ||||||
|
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 | 2026-09-03 04:54:13 | 8 | |||||||
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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 | 2026-09-03 04:54:27 | 4 | |||||||
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ClustVis Resource Report Resource Website 500+ mentions Issue |
ClustVis (RRID:SCR_017133) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps. | visualizing, clustering, multivariate, data, principal, component, analysis, plot, heatmap, bio.tools |
uses: Shiny uses: ggplot2 uses: pheatmap uses: RColorBrewer uses: FactoMineR is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing has parent organization: University of Tartu; Tartu; Estonia |
EFPIA ; Estonian Research Council ; European Commission ; European Federation of Pharmaceutical Industries and Associations ; European Regional Development Fund ; European Union Seventh Framework Programme ; Innovative Medicines Initiative Joint Undertaking |
PMID:25969447 | biotools:clustvis, OMICS_08539 | https://github.com/taunometsalu/ClustVis, https://bio.tools/clustvis | SCR_017133 | 2026-09-03 04:54:27 | 974 |
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