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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Program MARK Resource Report Resource Website 1+ mentions |
Program MARK (RRID:SCR_019281) | data analysis software, data processing software, software resource, software application | Software tool to provide parameter estimates from marked animals when they are re-encountered at later time, to create population size estimates. Used for analysis of data from marked individuals. | Parameter estimates, marked animal, marked animal data, re-encountered animals, population size estimates | has parent organization: Colorado State University; Colorado; USA | Free, Available for download, Freely available | SCR_019281 | 2026-08-13 09:30:22 | 4 | ||||||||||
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SCIGA Resource Report Resource Website 10+ mentions |
SCIGA (RRID:SCR_021002) | data analysis software, data processing software, software application, software toolkit, software resource | Software Perl toolkit for 10X single cell immunoglobulin repertoires analysis. Uses raw reads or output of Cellranger as input and performs reads quality control, immunoglobulin sequence assembly, sequence annotation, heavy- and light- chain pairing, computing statistics and visualizing. | 10X single cell immunoglobulin repertoires analysis, quality control, immunoglobulin sequence assembly, sequence annotation, heavy and light chain pairing, computing statistics, visualizing. | Free, Available for download, Freely available | biotools:sciga | https://bio.tools/sciga | SCR_021002 | SCIGA_v1.0.0.tar.gz | 2026-08-13 09:30:38 | 10 | ||||||||
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Allen Mouse Reference Atlas Ontology Resource Report Resource Website 1+ mentions |
Allen Mouse Reference Atlas Ontology (RRID:SCR_021000) | ontology, data or information resource, controlled vocabulary | Developed for Allen Reference Atlas and follows terminology from Brain Maps: Structure for the Rat Brain (Swanson, 2004, 2018). The ontology has been subsequently extended and revised to also serve as structure ontology for Allen Mouse Common Coordinate Framework.Defines hierarchical partonomy of anatomical structures of adult mouse brain. At top level, brain is divided into gray matter, fiber tracts and ventricular systems. Gray matter is subdivided into cerebrum, brain stem, and cerebellum, which are themselves organized into subregions in hierarchical tree. | structure ontology, brain structure, ontology, hierarchical partonomy, anatomical structures |
is used by: Allen Mouse Brain Common Coordinate Framework is used by: Early Postnatal Developmental Mouse Brain Atlas has parent organization: Allen Institute for Brain Science |
PMID:32386544 | Free, Freely available | SCR_021000 | 2026-08-13 09:30:24 | 5 | |||||||||
|
Flowlogic Resource Report Resource Website 50+ mentions |
Flowlogic (RRID:SCR_020942) | data analysis software, data processing software, software resource, software application | Software tool for flow cytometry data analysis by Miltenyi Biotec. | Flow cytometry data, data analysis, flow cytometry, Miltenyi Biotec | is listed by: SoftCite | Restricted | SCR_020942 | Flowlogic TM Software, Flowlogic Software | 2026-08-13 09:30:19 | 81 | |||||||||
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BrainVision PyCorder Resource Report Resource Website 50+ mentions |
BrainVision PyCorder (RRID:SCR_019286) | data acquisition software, data processing software, software resource, software application | Open source acquisition program, based on Python programming language, for setting up BrainVision actiCHamp amplifier and storing data. | Acquision Python program, setting up actiCHamp amplifier, BrainVision | https://www.brainlatam.com/manufacturers/brain-products/pycorder-127 | SCR_019286 | PyCorder | 2026-08-13 09:30:22 | 55 | ||||||||||
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SIMR Resource Report Resource Website 1+ mentions |
SIMR (RRID:SCR_019287) | data analysis software, data processing software, software application, software toolkit, software resource | Software R package for power analysis of generalized linear mixed models by simulation. Used to calculate power for generalised linear mixed models. | Power analysis, generalized linear mixed models, calculate power, simulation | is listed by: CRAN | New Zealand Ministry of Business ; Innovation and Employment |
DOI:10.1111/2041-210X.12504 | Free, Available for download, Freely available | https://github.com/pitakakariki/simr | SCR_019287 | simr, simR | 2026-08-13 09:30:19 | 4 | ||||||
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CiteFuse Resource Report Resource Website 1+ mentions |
CiteFuse (RRID:SCR_019321) | data analysis software, data processing software, software resource, software application | Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data. | Data pre processing, modality integration, clustering, differential RNA, ADT, expression analysis, ADT evaluation, ligand receptor interaction analysis, CITE-seq data, cellular indexing of transcriptomes and epitopes by sequencing, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian has parent organization: University of Sydney; Sydney; Australia |
PMID:32353146 | Free, Available for download, Freely available | biotools:citefuse | https://bioconductor.org/packages/CiteFuse/, https://github.com/SydneyBioX/CiteFuse/, http://shiny.maths.usyd.edu.au/CiteFuse/, https://bio.tools/CiteFuse | SCR_019321 | Cellular Indexing of Transcriptomes and Epitopes Fuse, Cellular indexing of transcriptomes and epitopes Fuse | 2026-08-13 09:30:23 | 3 | ||||||
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Bs-Seeker2 Resource Report Resource Website 1+ mentions |
Bs-Seeker2 (RRID:SCR_020948) | data analysis software, data processing software, software application, software resource, sequence analysis software | Software tool as versatile aligning pipeline for bisulfite sequencing data. Used for mapping bisulfite sequencing data and generating DNA methylomes. Improves mappability over existing aligners by using local alignment. Maps reads from RRBS library by building special indexes with improved efficiency and accuracy. Provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing overestimation of DNA methylation levels. | Versatile aligning pipeline, bisulfite sequencing data, mapping bisulfite sequencing data, generating DNA methylomes, DNA methylation level, reads mapping, Reduced Represented Bisulfite Sequencing library, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: BS Seeker has parent organization: University of California at Los Angeles; California; USA |
Institute of Genomics and Proteomics at UCLA ; NBRPC 2012CB316503; China Scholarship Council |
PMID:24206606 | Free, Available for download, Freely available | biotools:bs-seeker2 | http://pellegrini.mcdb.ucla.edu/BS_Seeker2/, https://bio.tools/bs-seeker2 | SCR_020948 | Bisulfite Sequencing Seeker2, BS Seeker2 | 2026-08-13 09:30:38 | 2 | |||||
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Expyfun Resource Report Resource Website 1+ mentions |
Expyfun (RRID:SCR_019285) | software toolkit, software resource, software library | Auditory and visual stimulus delivery library for psychoacoustics in Python. | Auditory, visual stimulus, stimulus delivery, library, psychoacoustics, Python. | Free, Available for download | SCR_019285 | 2026-08-13 09:30:37 | 1 | |||||||||||
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MITE-Hunter Resource Report Resource Website 1+ mentions |
MITE-Hunter (RRID:SCR_020946) | data analysis software, data processing software, software application, software resource, sequence analysis software | Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences. | Class 2 non-autonomous transposable element, genes non-coding regions, genome evolution, coding sequence, genomic DNA data sets, | NSF 0607123 | PMID:20880995 | Free, Available for download, Freely available | https://github.com/jburnette/MITE-Hunter | SCR_020946 | Miniature Inverted repeat Transposable Elements Hunter | 2026-08-13 09:30:23 | 7 | |||||||
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BayesEpiModels Web App Resource Report Resource Website 1+ mentions |
BayesEpiModels Web App (RRID:SCR_019292) | web application, analysis service resource, production service resource, service resource, software resource | Web app to help assess both short- and long-term forecasts of COVID-19 across the United States at multiple levels. Done by implementing one time-series model (ARIMA), one compartmental models (basic SIR), and six classical growth models, which all yield satisfactory prediction results in the past and current pandemics at early stage. | COVID-19, SARS-CoV-2, stochastic growth model, stochastic SIR model, Bayesian inference, | Free, Freely available | SCR_019292 | 2026-08-13 09:30:22 | 1 | |||||||||||
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xiNET Resource Report Resource Website 10+ mentions |
xiNET (RRID:SCR_021010) | data processing software, data access protocol, software application, data visualization software, web service, software resource | Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains. | Crosslinking mass spectrometry data visualization, linkage sites, linked peptides, crosslinking reaction product display, crosslink network maps, maps with residue resolution | Wellcome Trust | PMID:25648531 | Free, Available for download, Freely available | http://github.com/colin-combe/crosslink-viewer | SCR_021010 | Crosslink Network Maps With Residue Resolution | 2026-08-13 09:30:20 | 20 | |||||||
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Biofactoid Resource Report Resource Website 1+ mentions |
Biofactoid (RRID:SCR_021011) | data or information resource, project portal, data access protocol, web service, knowledge environment resource, software resource, portal | Web tool for creating digital profile of scientific discoveries in article and connecting them to related research. Authors describe molecular interactions supported by their results, letting researchers explore first hand account of article findings and connect to related articles and knowledge. Web based system for scientists to compose structured representation of networks of interactions between genes, their products, and chemical compounds, represented using power of formal ontology. | Knowledge management, molecular interactions, pathway, compose network structured representation, digital profile, connect related articles, formal ontology |
is related to: Biological Pathways Exchange is related to: Biological Pathways Exchange has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard University; Cambridge; United States has parent organization: University of Oregon; Oregon; USA |
NHGRI U41HG006623; DARPA Big Mechanism |
Free, Freely available | SCR_021011 | 2026-08-13 09:30:38 | 1 | |||||||||
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cgmapotools Resource Report Resource Website 1+ mentions |
cgmapotools (RRID:SCR_020950) | data analysis software, data processing software, software resource, software application | Software package for DNA methylation analysis. Used for context-wise, gene-wise, bin-wise, region-wise and sample-wise analysis and visualizations. Used to improve precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. | DNA methylomes analysis, DNA methylomes, context-wise analysis, gene-wise analysis, bin-wise analysis, region-wise analysis, sample-wise analysis, bisulfite sequencing data, allele specific methylation detection | National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:28968643 | Free, Available for download, Freely available | SCR_020950 | 2026-08-13 09:30:19 | 3 | |||||||||
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immuneML Resource Report Resource Website 1+ mentions |
immuneML (RRID:SCR_021004) | data or information resource, analysis service resource, production service resource, service resource, portal | Open source Python platform for machine learning based analysis and classification of adaptive immune receptors and repertoires. Supported by ELIXIR Norway. | Immune receptor, machine learning, predicting immune status, predicting antigen specificity | DOI:10.1101/2021.03.08.433891 | Free, Available for download, Freely available | SCR_021007 | https://galaxy.immuneml.uio.no/, https://github.com/uio-bmi/immuneML | SCR_021004 | 2026-08-13 09:30:20 | 1 | ||||||||
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Hugging Face Resource Report Resource Website 100+ mentions |
Hugging Face (RRID:SCR_020958) | data or information resource, organization portal, community building portal, portal | Portal to build, train and deploy state of the art models powered by reference open source in natural language processing. | Hugging Face, Inc., NLP, Natural Language Processing, build art models, deploy art models, reference open source | Free, Freely available | https://github.com/huggingface | SCR_020958 | 2026-08-13 09:30:19 | 121 | ||||||||||
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spdep Resource Report Resource Website 1+ mentions |
spdep (RRID:SCR_019294) | data analysis software, data processing software, software application, software toolkit, software resource | Software R package as collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree. | Spatial weights matrix objects, spatial dependence, weighting schemes, spatial weights, matrix objects | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/r-spatial/spdep/ | SCR_019294 | Spatial Dependence: Weighting Schemes and Statistics, spatial dependence | 2026-08-13 09:30:37 | 2 | ||||||||
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MesKit Resource Report Resource Website 1+ mentions |
MesKit (RRID:SCR_020959) | data analysis software, data processing software, software application, software toolkit, data visualization software, software resource, sequence analysis software | Software R package for dissecting cancer evolution from multi region derived tumor biopsies via somatic mutations. Used for characterizing cancer genomic ITH and inferring history of tumor evolution via implementation of well established computational and statistical methods. | Dissecting cancer evolution, region derived tumor biopsies, somatic mutations, cancer genomic ITH, tumor evolution | has parent organization: Sun Yat-sen University; Guangdong; China | Free, Available for download, Freely available | https://bioconductor.org/packages/MesKit/ | SCR_020959 | Multi region exome sequencing analysis tool Kit | 2026-08-13 09:30:38 | 4 | ||||||||
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scales Resource Report Resource Website 10+ mentions |
scales (RRID:SCR_019295) | data processing software, software application, software toolkit, data visualization software, software resource | Software R package as scale functions for visualization. Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends. | Scale functions, visualization, graphical scales, map data, axes, determining breaks, legend, determining labels | Free, Available for download, Freely available | https://github.com/r-lib/scales | SCR_019295 | 2026-08-13 09:30:22 | 18 | ||||||||||
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exRNA Atlas Resource Report Resource Website 10+ mentions |
exRNA Atlas (RRID:SCR_017221) | ontology, data or information resource, organization portal, data access protocol, application programming interface, controlled vocabulary, consortium, analysis service resource, expression atlas, atlas, production service resource, database, service resource, data repository, storage service resource, data analysis service, software resource, portal | Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data. | Differential, expression, RNA, sequencing, qPCR, data, visualization, extracellular, exRNA, atlas, repository, dataset |
is recommended by: National Library of Medicine has parent organization: Baylor College of Medicine; Houston; Texas has parent organization: exRNA |
gastric cancer, colon carcinoma, colorectal cancer, prostate carcinoma, pancreatic carcinoma, multiple sclerosis, glioblastoma multiforme, ulcerative colitis, Alzheimer's disease, ischemic stroke, intraparenchymal hemorrhage of brain, asthma, cardiovascular disorder, myocardial infarction, lupus, nephrotic syndrome, transplanted kidney present, liver disease, transplanted liver present, pre-eclampsia, Parkinson disease, intraventricular brain hemorrhage, subarachnoid hemorrhage | NIDA U54 DA036134; NCI R01 CA163849; NIGMS R25 GM056929; NCATS UH3 TR000906; NCI U19 CA179512; NIDDK P30 DK63720; NHLBI K23 HL127099; NHLBI R01 HL136685; NIA R01 AG059729; NCATS UH3 TR000943; NCI R35 CA209904; NCI CA217685; NHLBI R01 HL122547; American Cancer Society ResearchProfessor Award ; Frank McGraw Memorial Chair in CancerResearch |
PMID:30951672 | Restricted | SCR_017221 | 2026-08-13 09:30:01 | 29 |
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