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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PathVisio Resource Report Resource Website 10+ mentions |
PathVisio (RRID:SCR_023789) | data processing software, data visualization software, software application, software resource, software toolkit | Software visualization tool for biological pathways. Pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. Developed in Java and can be extended with plugins. | biological pathway editor, pathway editor, visualization and analysis, extendable pathway analysis, | Netherlands Consortium for Systems Biology ; NHGRI HG003053; NIGMS GM080223; NIGMS R01 GM100039; Transnational University Limburg |
PMID:25706687 PMID:18817533 |
Free, Available for download, Freely available | SCR_023789 | SciCrunch Registry | PathVisio 3 | 2026-10-24 12:49:35 | 27 | ||||||||
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Health Information National Trends Survey Resource Report Resource Website 50+ mentions |
Health Information National Trends Survey (RRID:SCR_023943) | HINTS | data or information resource, disease-related portal, portal, topical portal | Regularly collects nationally representative data about American public’s knowledge of, attitudes toward, and use of cancer and health related information. HINTS data are used to monitor changes in fields of health communication and health information technology and to create more effective health communication strategies across different populations. Weighted, nationally representative probability based survey of civilian, non-institutionalized adults administered by National Cancer Institute on knowledge of and attitudes toward cancer relevant information. | National Cancer Institute, HINTS data, American public’s knowledge, cancer relevant information, use of cancer and health related information, survey of civilian and non-institutionalized adults, | cancer | Free, Freely available | SCR_023943 | SciCrunch Registry | Health Information National Trends Survey (HINTS), The Health Information National Trends Survey (HINTS) | 2026-10-24 12:49:37 | 52 | ||||||||
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Customized Guide Cannulas Resource Report Resource Website |
Customized Guide Cannulas (RRID:SCR_023941) | instrument resource | Open source modular apparatus to produce guide cannulas exploiting 3D printing technology. Step by step procedure to realize hippocampal guide cannulas. 3D-printed guide cannula implant, as well as rotary tool based cutting station for fabrication of cannulae. Useful to conduct research in all the fields where access to brain areas is needed. | OpenBehavior, apparatus, 3D-printed guide cannula implant, produce guide cannulas, brain 3D printing, hippocampal guide cannulas, hippocampal guide cannulas procedure, neuroscience, | is listed by: OpenBehavior | PMID:36104275 | Free, Freely available | SCR_023941 | SciCrunch Registry | 2026-10-24 12:49:37 | 0 | |||||||||
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Allen Mouse Brain ImageLoader Resource Report Resource Website |
Allen Mouse Brain ImageLoader (RRID:SCR_023827) | software resource | Respository contains two small software tools which render annotation and images of the Allen Mouse Brain Atlas. Both tools generate 1304 images of the Mouse Brain (456 sagital, 528 coronal and 320 axial). | Allen Mouse Brain Atlas, render annotation and images, mouse brain images, mouse brain images generation, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023827 | SciCrunch Registry | 2026-10-24 12:49:35 | 0 | ||||||||||
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IGoR Resource Report Resource Website 10+ mentions |
IGoR (RRID:SCR_024053) | data analysis software, data processing software, software application, software resource | C++ software designed to infer V(D)J recombination related processes from sequencing data. | infer V(D)J recombination related processes, sequencing data, | is listed by: Debian | PMID:29422654 | Free, Available for download, Freely available, | OMICS_18534 | https://sources.debian.org/src/igor/, https://qmarcou.github.io/IGoR/ | SCR_024053 | SciCrunch Registry | Inference and Generation Of Repertoires, igor | 2026-10-24 12:49:38 | 13 | ||||||
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Proteinortho Resource Report Resource Website 50+ mentions |
Proteinortho (RRID:SCR_024177) | data analysis software, data processing software, software application, software resource | Software tool to detect orthologous genes within different species. Stand-alone tool for large datasets for orthology analysis. | Stand-alone tool, detect orthologous genes, different species, large datasets, orthology analysis, | is listed by: Debian | PMID:21526987 | Free, Available for download, Freely available, | OMICS_05355 | https://sources.debian.org/src/proteinortho/ | SCR_024177 | SciCrunch Registry | 2026-10-24 12:49:39 | 99 | |||||||
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KmerResistance Resource Report Resource Website 1+ mentions |
KmerResistance (RRID:SCR_024058) | data analysis software, data processing software, software application, software resource | Software tool to correlate mapped genes with the predicted species of WGS samples, where this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available. | correlate mapped genes, predicted species, WGS samples, identification of genes, | is listed by: Debian | PMID:27365186 | Free, Available for download, Freely available, | https://sources.debian.org/src/kmerresistance/ | SCR_024058 | SciCrunch Registry | kmerresistance | 2026-10-24 12:49:38 | 1 | |||||||
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PROFisis Resource Report Resource Website |
PROFisis (RRID:SCR_024179) | simulation software, software application, software resource | Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures. | identifies interacting residues from sequence alone, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_13706 | https://sources.debian.org/src/profisis/ | SCR_024179 | SciCrunch Registry | profisis | 2026-10-24 12:49:39 | 0 | |||||||
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Ambulatory Monitoring: Psychomotor Vigilance Task system Resource Report Resource Website 1+ mentions |
Ambulatory Monitoring: Psychomotor Vigilance Task system (RRID:SCR_024213) | instrument resource | System includes PVT-192 monitor and REACT software. Used for reaction time testing for long-term, large-scale testing of vigilance, effects of sleep deprivation, and drug effects. Used for PVT test wherever measures of performance or sleepiness effects are needed. | Ambulatory Monitoring Inc., reaction time testing, PVT-192 monitor, REACT software, testing of vigilance, effects of sleep deprivation, drug effects, PVT test, sleepiness effects measurement, instrument, equipment | DOI:10.3758/BF03200977 | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_024213.pdf | SCR_024213 | SciCrunch Registry | , Psychomotor Vigilance Task, PVT-192 Psychomotor Vigilance Task Monitor | 2026-10-24 12:49:39 | 1 | ||||||||
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ProDA Resource Report Resource Website 1+ mentions |
ProDA (RRID:SCR_024171) | alignment software, data processing software, image analysis software, software application, software resource | Software for multiple alignment of protein sequences with repeated and shuffled elements.Used for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures. | sequence alignment, protein sequences, protein sequences multiple alignment, repeated sequences, shuffled elements, | is listed by: Debian | DOI:10.1093/nar/gkl511 | Free, Available for download, Freely available, | OMICS_21692 | https://sources.debian.org/src/proda/ | SCR_024171 | SciCrunch Registry | proda | 2026-10-24 12:49:39 | 1 | ||||||
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Kleborate Resource Report Resource Website 10+ mentions |
Kleborate (RRID:SCR_024051) | data analysis software, data processing software, software application, software resource | Software tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for MLST sequence type, species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.), ICEKp associated virulence loci (yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)), virulence plasmid associated loci (salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)), antimicrobial resistance determinants (acquired genes, SNPs, gene truncations and intrinsic ?-lactamases), and K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive. | screen genome assemblies, Klebsiella pneumoniae, Klebsiella pneumoniae species complex, genome assemblies, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/kleborate/ | SCR_024051 | SciCrunch Registry | KLEBORATE, kleborate | 2026-10-24 12:49:38 | 27 | ||||||||
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VIGRA Resource Report Resource Website 1+ mentions |
VIGRA (RRID:SCR_024100) | , data processing software, image analysis software, image processing software, software application, software library, software resource, software toolkit | Software image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images. By using template techniques similar to those in the C++ Standard Template Library, you can easily adapt any VIGRA component to the needs of your application, without thereby giving up execution speed. As of version 1.7.1, VIGRA also provides extensive Python bindings on the basis of the popular numpy framework. | image processing and analysis library, customizable algorithms and data structures, multi-dimensional image, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libvigraimpex/ | SCR_024100 | SciCrunch Registry | , The VIGRA Computer Vision Library, Vision with Generic Algorithms, libvigraimpex | 2026-10-24 12:49:38 | 1 | ||||||||
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pynast Resource Report Resource Website 50+ mentions |
pynast (RRID:SCR_024189) | alignment software, data processing software, image analysis software, software application, software resource | Software tool for aligning sequences to template alignment. | aligning sequences to template alignment, | is listed by: Debian | PMID:19914921 | Free, Available for download, Freely available, | OMICS_15419 | https://sources.debian.org/src/pynast/ | SCR_024189 | SciCrunch Registry | Python Nearest Alignment Space Termination tool | 2026-10-24 12:49:40 | 65 | ||||||
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sigma-align Resource Report Resource Website 1+ mentions |
sigma-align (RRID:SCR_024337) | alignment software, data processing software, image analysis software, software application, software resource | Software alignment program with new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step. | alignment program, non-coding DNA sequence, | is listed by: Debian | PMID:16542424 | Free, Available for download, Freely available, | OMICS_29594 | https://sources.debian.org/src/sigma-align/ | SCR_024337 | SciCrunch Registry | Simple greedy multiple alignment | 2026-10-24 12:49:40 | 1 | ||||||
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signalalign Resource Report Resource Website 1+ mentions |
signalalign (RRID:SCR_024339) | alignment software, data processing software, image analysis software, software application, software resource | Software tool to align ionic current from MinION to reference sequence using trainable hidden Markov model. HMM-HDP models for MinION signal alignments, | Oxford Nanopore Technologies, MinION sequences DNA, align ionic current, reference sequence, trainable hidden Markov model, HMM-HDP models, MinION signal alignments, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/signalalign/ | SCR_024339 | SciCrunch Registry | 2026-10-24 12:49:40 | 2 | |||||||||
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scNTImpute Resource Report Resource Website 1+ mentions |
scNTImpute (RRID:SCR_024395) | data analysis software, data processing software, software application, software resource | Software imputation model for scRNA-seq data. Used to accurately and efficiently identify dropout values and impute them precisely, which helps to improve downstream analyses of single-cell RNA sequencing data. | imputation model, scRNA-seq data, identify dropout values, single-cell RNA sequencing data analysis, | Free, Available for download, Freely available, | SCR_024395 | SciCrunch Registry | single-cell Neural Topic Imputation | 2026-10-24 12:49:41 | 1 | ||||||||||
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Patristic Resource Report Resource Website 1+ mentions |
Patristic (RRID:SCR_024154) | data analysis software, data processing software, software application, software resource | Software Java program for calculating patristic distances and graphically comparing the components of genetic change. | calculating patristic distances, graphically comparing the components of genetic change, | is listed by: Debian | PMID:16388682 | Free, Available for download, Freely available, | https://sources.debian.org/src/patristic/ | SCR_024154 | SciCrunch Registry | patristic | 2026-10-24 12:49:38 | 5 | |||||||
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ChrAccR Resource Report Resource Website 1+ mentions |
ChrAccR (RRID:SCR_024397) | data analysis software, data processing software, software application, software resource | Software R package for comprehensive analysis chromatin accessibility data. Analyzing chromatin accessibility data in R. Used for data quality control, exploratory analyses including unsupervised methods for dimension reduction, clustering and quantifying transcription factor activities, and identification and characterization of differentially accessible regions. Used for analysis of large bulk datasets comprising hundreds of samples as well as for single cell datasets. | analysis chromatin accessibility data, data quality control, identification and characterization of differentially accessible regions, clustering and quantifying transcription factor activities, | Free, Available for download, Freely available | https://greenleaflab.github.io/ChrAccR/ | SCR_024397 | SciCrunch Registry | Chromatin Accessibility data in R | 2026-10-24 12:49:40 | 2 | |||||||||
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Efficient and Adaptive Gaussian Smoothing Resource Report Resource Website 1+ mentions |
Efficient and Adaptive Gaussian Smoothing (RRID:SCR_024399) | EAGS | data analysis software, data processing software, software application, software resource | Software tool for high resolved spatial transcriptomics. Smoothing approach for spatial transcriptome data with ultrahigh resolution. Used to determine neighborhood relationship of cells, to calculate smoothing contribution to recalculate the gene expression of each cell. | determine neighborhood cells relationship, calculate cell gene expression, high resolved spatial transcriptomics, spatial transcriptome data, data with ultrahigh resolution, | Free, Available for download, Freely available, | SCR_024399 | SciCrunch Registry | 2026-10-24 12:49:40 | 1 | ||||||||||
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ScanProsite Resource Report Resource Website 100+ mentions |
ScanProsite (RRID:SCR_024425) | PMID:16845026 | data access protocol, software resource, web service | Web tool for detecting PROSITE signature matches in protein sequences. | detecting PROSITE signature matches, protein sequences, | is listed by: SoftCite | Swiss National Science Foundation ; Swiss Federal Government |
Free, Freely available | https://www.expasy.org/resources/scanprosite | SCR_024425 | SciCrunch Registry | 2026-10-24 12:49:40 | 106 |
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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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