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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Anima Resource Report Resource Website 10+ mentions |
Anima (RRID:SCR_017017) | software application, image analysis software, data analysis software, data or information resource, diffusion-weighted mri 3d image, software resource, data processing software, registration software, image processing software, image, mri 3d image, 3d spatial image, software toolkit, portal | 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 | 2026-07-28 09:44:27 | 15 | |||||||||
|
smMIPfil Resource Report Resource Website 1+ mentions |
smMIPfil (RRID:SCR_016892) | software application, software resource, data analysis software, data processing software | 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 | 2026-07-28 09:44:25 | 2 | |||||||||
|
Thunder STORM Resource Report Resource Website 10+ mentions |
Thunder STORM (RRID:SCR_016897) | ThunderSTORM | software application, data analysis software, software resource, data processing software, 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 |
Czech Science Foundation ; Charles University ; European Regional Development Fund ; European Social Fund |
PMID:24771516 | Free, Available for download, Freely available | biotools:thunderstorm | https://bio.tools/thunderstorm | SCR_016897 | 2026-07-28 09:44:25 | 42 | |||||
|
CRISPR-P Resource Report Resource Website 10+ mentions |
CRISPR-P (RRID:SCR_016941) | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | 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 |
National Basic Research Program of China ; Program for New Century Excellent Talents in University ; Fundamental Research Funds for the Central Universities |
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 | 2026-07-28 09:44:26 | 30 | |||||
|
ascat Resource Report Resource Website 10+ mentions |
ascat (RRID:SCR_016868) | ASCAT | software application, software resource, data analysis software, data processing software | 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 | 2026-07-28 09:44:24 | 33 | |||||
|
Pyclone Resource Report Resource Website 10+ mentions |
Pyclone (RRID:SCR_016873) | software application, software resource, data analysis software, data processing software | 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 | 2026-07-28 09:44:25 | 42 | ||||||||
|
Metab Resource Report Resource Website 1+ mentions |
Metab (RRID:SCR_016877) | Metab | software application, data analysis software, software resource, data processing software, 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 | 2026-07-28 09:44:25 | 1 | ||||||
|
OpenBMI Resource Report Resource Website 1+ mentions |
OpenBMI (RRID:SCR_016876) | software application, data analysis software, software resource, data processing software, data visualization software, 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 | 2026-07-28 09:44:25 | 5 | |||||||||
|
Phenograph Resource Report Resource Website 100+ mentions |
Phenograph (RRID:SCR_016919) | PhenoGraph | software application, software resource, data analysis software, data processing software | 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 |
NIGMS R00 GM104148; NICHD DP1 HD084071; NCI R01 CA164729; NCI U54 CA121852; NCI R01 CA130826; NCI U54 CA143907; US Department of Health and Human Services HHSN272200700038C; NIH N01 HV00242; NCI P01 CA034233; NIAID U19 AI057229; NCI U54 CA149145; US FDA HHSF223201210194C; US DOD W81XWH1210591; Entertainment Industry Foundation ; Rachford and Carlota Harris Endowed Professorship ; CIRM DR1 01477; CIRM RB201592; Stand Up To Cancer Phillip A. Sharp Award SU2CAACRPS04; Packard Fellowship for Science and Engineering ; NIH Office of the Director DP2 OD002414 |
PMID:26095251 | Free, Available for download, Freely available | https://github.com/JinmiaoChenLab/Rphenograph | https://github.com/jacoblevine/PhenoGraph | SCR_016919 | 2026-07-28 09:44:26 | 213 | |||||
|
clusterProfiler Resource Report Resource Website 10000+ mentions |
clusterProfiler (RRID:SCR_016884) | software application, data analysis software, software resource, data processing software, data visualization software | 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 |
National 973 Projects of China ; 2007 Chang-Jiang Scholars Program ; National Natural Science Foundation of China ; Guangdong Natural Science Research Grant ; Fundamental Research Funds for the Central Universities |
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 | 2026-07-28 09:44:28 | 10762 | |||||
|
affydata Resource Report Resource Website |
affydata (RRID:SCR_016976) | AffyData | software application, data analysis software, data or information resource, software resource, data processing software | 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 | 2026-07-28 09:44:30 | 0 | ||||||||
|
CCPN Analysis Resource Report Resource Website 10+ mentions |
CCPN Analysis (RRID:SCR_016984) | CcpNmr Analysis | software application, data analysis software, software resource, data processing software, data visualization software | 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 |
Deutsche Forschungsgemeinschaft ; Biotechnology and Biological Sciences Research Council (UK) |
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 | 2026-07-28 09:44:27 | 47 | ||||||
|
Signal Resource Report Resource Website 10+ mentions |
Signal (RRID:SCR_017081) | software application, data analysis software, software resource, data processing software, data acquisition software | 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 | 2026-07-28 09:44:29 | 13 | ||||||||||
|
ImmuneDB Resource Report Resource Website 1+ mentions |
ImmuneDB (RRID:SCR_017125) | service resource, data or information resource, data analysis service, database, production service resource, analysis 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 | NIAID P01 AI106697; NIAID P30 AI0450080; NIDDK UC4 DK112217; NCI P30 CA016520 |
PMID:30298069 | Free, Available for download, Freely available | https://github.com/arosenfeld/immunedb | SCR_017125 | 2026-07-28 09:44:31 | 8 | |||||||
|
Scikit-Criteria Resource Report Resource Website |
Scikit-Criteria (RRID:SCR_017084) | software library, software toolkit, software resource | 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 | 2026-07-28 09:44:26 | 0 | |||||||||
|
SwiftOrtho Resource Report Resource Website 1+ mentions |
SwiftOrtho (RRID:SCR_017122) | software application, software resource, data analysis software, data processing software | 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 | 2026-07-28 09:44:31 | 4 | |||||||
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Haystack Resource Report Resource Website 1+ mentions |
Haystack (RRID:SCR_017087) | software application, data analysis software, software resource, data processing software, 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 | 2026-07-28 09:44:26 | 3 | ||||||||
|
ClustVis Resource Report Resource Website 500+ mentions Issue |
ClustVis (RRID:SCR_017133) | service resource, data analysis service, data access protocol, software resource, production service resource, web service, analysis service resource | 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 |
Innovative Medicines Initiative Joint Undertaking ; European Union Seventh Framework Programme ; European Federation of Pharmaceutical Industries and Associations ; European Regional Development Fund ; Estonian Research Council ; European Commission ; EFPIA |
PMID:25969447 | biotools:clustvis, OMICS_08539 | https://github.com/taunometsalu/ClustVis, https://bio.tools/clustvis | SCR_017133 | 2026-07-28 09:44:31 | 798 | |||||||
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University of North Carolina Charlotte Bioinformatics Services Division Resource Report Resource Website |
University of North Carolina Charlotte Bioinformatics Services Division (RRID:SCR_017182) | BiSD, UNC Charlotte BiSD | service resource, data or information resource, data analysis service, production service resource, access service resource, analysis service resource, core facility | Core to assist with analyzing and interpreting data produced by genomic technologies. | bioinformatics, analysis, data, genomic | Open | SCR_017182 | , Charlotte, University of North Carolina, BiSD, Bioinformatics Services Division, UNC | 2026-07-28 09:44:31 | 0 | |||||||||
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GAGE Resource Report Resource Website 50+ mentions |
GAGE (RRID:SCR_017067) | software application, software resource, data analysis software, data processing software | 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 | 2026-07-28 09:44:28 | 50 |
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