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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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MindTheGap Resource Report Resource Website 1+ mentions |
MindTheGap (RRID:SCR_024115) | data analysis software, data processing software, software application, software resource | Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. | perform detection and assembly of DNA insertion variants, NGS read datasets, reference genome, call insertions, donor genome, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_05472 | https://sources.debian.org/src/mindthegap/ | SCR_024115 | SciCrunch Registry | mindthegap | 2026-09-26 02:17:33 | 3 | |||||||
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MafFilter Resource Report Resource Website 10+ mentions |
MafFilter (RRID:SCR_024105) | data analysis software, data processing software, software application, software resource | Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc. | genome alignments analysis, parse and manipulate MAF files, genome alignment processor, | is listed by: Debian | PMID:24447531 | Free, Available for download, Freely available, | OMICS_06743 | https://sources.debian.org/src/maffilter/, https://github.com/jydu/maffilter | SCR_024105 | SciCrunch Registry | MafFilter a genome alignment processor, maffilter | 2026-09-26 02:17:33 | 12 | ||||||
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sparta Resource Report Resource Website 10+ mentions |
sparta (RRID:SCR_024349) | data analysis software, data processing software, software application, software resource | Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms. | analyzing single-end Illumina RNA-seq data, | is listed by: Debian | PMID:26847232 | Free, Available for download, Freely available, | https://sources.debian.org/src/sparta/ | SCR_024349 | SciCrunch Registry | SPARTA | 2026-09-26 02:17:34 | 10 | |||||||
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Maude Resource Report Resource Website |
Maude (RRID:SCR_024108) | data or information resource, portal, project portal, software library, software resource, software toolkit | Software high performance reflective language and system supporting both equational and rewriting logic specification and programming for wide range of applications.Supports equational specification and programming, rewriting logic computation. | equational and rewriting logic specification and programming, equational specification and programming, rewriting logic computation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/maude/, http://maude.cs.illinois.edu/w/index.php/Maude_download_and_installation | SCR_024108 | SciCrunch Registry | Maude, maude | 2026-09-26 02:17:33 | 0 | ||||||||
|
mPTP Resource Report Resource Website 1+ mentions |
mPTP (RRID:SCR_024121) | data analysis software, data processing software, software application, software resource | Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets. | single locus species delimitation, ML delimitation from inferred phylogenetic tree of the samples, ML delimitation, inferred phylogenetic tree, samples inferred phylogenetic tree, | is listed by: Debian | PMID:28108445 | Free, Available for download, Freely available, | OMICS_15264 | https://sources.debian.org/src/mptp/ | SCR_024121 | SciCrunch Registry | , mptp, multi-rate Poisson Tree Processes | 2026-09-26 02:17:33 | 2 | ||||||
|
Yanosim Resource Report Resource Website |
Yanosim (RRID:SCR_024363) | Yanosim | simulation software, software application, software resource | Software tool as read simulator for nanopore DRS datasets. | read simulator for nanopore DRS datasets, read simulator, nanopore DRS datasets, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/yanosim/ | SCR_024363 | SciCrunch Registry | yanosim, yet another nanopore simulator | 2026-09-26 02:17:34 | 0 | |||||||
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Molekel Resource Report Resource Website 1+ mentions |
Molekel (RRID:SCR_024122) | data processing software, data visualization software, software application, software resource | Open source multi platform molecular visualization program. | molecular visualization | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/molekel/ | SCR_024122 | SciCrunch Registry | molekel | 2026-09-26 02:17:33 | 1 | ||||||||
|
MRtrix3 Resource Report Resource Website 100+ mentions |
MRtrix3 (RRID:SCR_024123) | data analysis software, data processing software, software application, software resource | Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses. | diffusion MRI analyses, tractography, next generation group level analyses, | is listed by: Debian | PMID:31473352 | Free, Available for download, Freely available, | https://sources.debian.org/src/mrtrix3/ | SCR_024123 | SciCrunch Registry | mrtrix3 | 2026-09-26 02:17:33 | 335 | |||||||
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MIA Resource Report Resource Website |
MIA (RRID:SCR_024081) | data processing software, image analysis software, software application, software resource | Software toolkit for gray scale medical image analysis. Provides combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in command shell and prototype algorithms as shell scripts. MIA is build around a plug-in structure that makes it easy to add functionality without compromising the original code base, and it makes use of wide variety of external libraries that provide additional functionality. | gray scale medical image analysis, interactive image processing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/mia/ | https://sources.debian.org/src/libmialm/ | SCR_024081 | SciCrunch Registry | python3-mia, libmia-2.4-dev, mia-tools, mia-viewit, libvistaio-dev, libmialm-dev, libmiaviewit-dev, libmialm, mialmpick | 2026-09-26 02:17:33 | 0 | |||||||
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iMaps Resource Report Resource Website 10+ mentions |
iMaps (RRID:SCR_016705) | analysis service resource, data analysis service, data or information resource, portal, production service resource, service resource | Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions. | Genialis, analysis, high-resolution, sequencing, data, RNA, DNA, protein, interaction |
is related to: iCount is related to: iCount |
Free, Registration required | SCR_016705 | SciCrunch Registry | 2026-09-26 02:15:50 | 11 | ||||||||||
|
Zeiss: libra 120 transmission electron microscope Resource Report Resource Website 1+ mentions |
Zeiss: libra 120 transmission electron microscope (RRID:SCR_016703) | instrument resource | Electron microscope by Carl Zeiss AG which combines flexibility and ease of use of new control electronics, Windows® based user interface and a vacuum system. | instrument, electron, microscope, Carl Zeiss | Commercially available | https://drive.google.com/file/d/1sgiYV8KlKkLXagtcEe1d-Oh7y0_GncP6/view?usp=drivesdk | https://www.binran.ru/files/ckp/tem/CKP_Libra%20120%20en_User%20Manual.pdf | SCR_016703 | SciCrunch Registry | Carl Zeiss AG - LIBRA 120, libra 120, The LIBRA 120 | 2026-09-26 02:15:51 | 1 | ||||||||
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Gallios: Flow Cytometer Resource Report Resource Website 1+ mentions |
Gallios: Flow Cytometer (RRID:SCR_016702) | instrument resource | Instrument provides acquisition of up to 12 parameters with optical design for enhanced sensitivity for multicolor assays. With customized forward scatter, to achieve accurate size measurement, and optimized electronics for high resolution and fast, accurate processing for researchers needs. | instrument, coulter, flow, cytometer, multicolor, assay, cell, processing, parameter, acquisition | Commercially available | https://www.beckman.de/en/coulter-flow-cytometers/gallios/ | SCR_016702 | SciCrunch Registry | 2026-09-26 02:15:50 | 1 | ||||||||||
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Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/, https://bio.tools/pavian | SCR_016679 | SciCrunch Registry | 2026-09-26 02:15:50 | 33 | ||||||
|
iCount Resource Report Resource Website 10+ mentions |
iCount (RRID:SCR_016712) | data analysis software, data processing software, software application, software resource | Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps. | protein, RNA, interaction, analysis, iCLIP, sequencing, data, map |
is related to: iMaps is related to: iMaps |
Free, Available for download, Freely available, Tutorial available | https://icount.readthedocs.io/en/latest/ref_python.html, https://hub.docker.com/r/tomazc/icount/ | SCR_016712 | SciCrunch Registry | 2026-09-26 02:15:50 | 39 | |||||||||
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Neuronexus: Neural Probe A1x16-3mm-100-703 Resource Report Resource Website |
Neuronexus: Neural Probe A1x16-3mm-100-703 (RRID:SCR_016678) | instrument resource | Instrument as a 16 channel linear electrode array from NeuroNexus Technologies, Ann Arbor, Michigan. Used to map brain function, detect neural activity, and stimulate or modulate neural circuits when brain function is impaired. Used for small and large animal models for neuroscience and clinical applications. | NeuroNexus, Matrix Array, neural, probe, 16 channel, linear, electrode, array, map, brain, function | Commercially available | http://neuronexus.com/electrode-array/a1x16-3mm-100-703/ | SCR_016678 | SciCrunch Registry | 2026-09-26 02:15:50 | 0 | ||||||||||
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INC-Seq Resource Report Resource Website |
INC-Seq (RRID:SCR_016711) | INC-Seq | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for accurate single molecule reads using nanopore sequencing. Used for 16S rRNA-based profiling to investigate complex bacterial communities. | accurate, single, molecule, read, nanopore, sequencing, 16S rRNA, bacteria | is related to: NanoAmpli-Seq | Agency for Science ; Technology and Research ; Singapore |
PMID:27485345 | Free, Available for download, Freely available | https://zenodo.org/record/57405#.W-nb0pNKiM8 | SCR_016711 | SciCrunch Registry | Intramolecular ligated Nanopore Consensus Sequencing, INC-Seq | 2026-09-26 02:15:50 | 0 | |||||
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A-M SYSTEMS: Model 2100 Isolated Pulse Stimulator Resource Report Resource Website 1+ mentions |
A-M SYSTEMS: Model 2100 Isolated Pulse Stimulator (RRID:SCR_016677) | instrument resource | Instrument used for a variety of physiological stimulation protocols, including behavioral feedback, LTP/LTD, lesion making, electrode marking, ultrafast timing applications, orthodromic/antidromic stimulation, and kindling. Used in a neurophysiological and physiological experiment protocols. | A-M Systems, stimulation, instrument, neurophysiological, physiological, experiment, protocol | Commercially available | https://drive.google.com/file/d/1sN9NYzMciABPPgk09f3cVZDrhiJfak24/view?usp=drivesdk | https://www.a-msystems.com/pub/manuals/2100manual.pdf | SCR_016677 | SciCrunch Registry | 2026-09-26 02:15:50 | 6 | |||||||||
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NanoAmpli-Seq Resource Report Resource Website 1+ mentions |
NanoAmpli-Seq (RRID:SCR_016710) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for a workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Used for full-length SSU rRNA gene sequencing. | amplicon, sequencing, 16S rRNA, mixed, microbial, communities, nanopore, platform, gene |
is related to: INC-Seq has parent organization: University of Glasgow; Glasgow; United Kingdom |
EPSRC EP/M016811/1; NERC NE/L011956/1 |
DOI:10.1101/244517 | Free, Available for download, Freely available | https://www.protocols.io/view/nanoampli-seq-bioinformatics-workflow-u25eyg6 | SCR_016710 | SciCrunch Registry | 2026-09-26 02:15:50 | 1 | |||||||
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | data analysis software, data processing software, data visualization software, image analysis software, software application, software resource | Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures. | biological, image, data, visualization, analysis, tracing, single, neuron, 3D, structure, brain |
is listed by: OMICtools is listed by: CRAN is related to: R Project for Statistical Computing is related to: elmr has parent organization: University of Cambridge; Cambridge; United Kingdom |
DOI:10.5281/zenodo.10171 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/nat/index.html, | SCR_016716 | SciCrunch Registry | NeuroAnatomy Toolbox, neuroanatomy toolbox, Neuro Anatomy Toolbox, neuro anatomy toolbox | 2026-09-26 02:15:50 | 5 | ||||||
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Florida State University Physical Biochemistry Core Facility Resource Report Resource Website 1+ mentions |
Florida State University Physical Biochemistry Core Facility (RRID:SCR_016714) | PBF | access service resource, availability annotation standard, core facility, data or information resource, material service resource, narrative resource, nif annotation standard, production service resource, service resource, standard specification, the community can contribute to this resource, training service resource | Facility for biophysical studies of macromolecules with emphasis on providing resources, instrumentation, training, and guidance to graduate and undergraduate students. | core, facility, biophysical, study, macromolecule, providing, resource, instrument, training, guidance, student, Florida, State, University |
has parent organization: Florida State University; Florida; USA has parent organization: Institute of Molecular Biophysics at Florida State University; Florida; USA |
Restricted | SCR_016714 | SciCrunch Registry | The Physical Biochemistry Facility (PBF), The Physical Biochemistry Facility, Physical Biochemistry Facility | 2026-09-26 02:15:51 | 1 |
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