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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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PolyPhen: Polymorphism Phenotyping Resource Report Resource Website 1000+ mentions |
PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) | PolyPhen, PolyPhen-2, POLYPHEN | data analysis software, data processing software, simulation software, software application, software resource | Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs. | annotate, nonsynonymous, SNP, predict, coding, damaging, effect, missense, mutation, sequence, variant, phenotype, genetic, disease, exon, protein, coding, fraction, genome, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Harvard University; Cambridge; United States |
PMID:20354512 PMID:23315928 |
SCR_013200, OMICS_00136, nlx_154540, nif-0000-21329, biotools:polyphen, SCR_013238 | https://bio.tools/polyphen | http://www.bork.embl-heidelberg.de/PolyPhen/ | SCR_013189 | SciCrunch Registry | PolyPhen, POLYPHEN, PolyPhen-2, Polymorphism Phenotyping, Polymorphism Phenotyping v2 | 2026-10-24 12:47:01 | 4723 | |||||
|
Crossbow Resource Report Resource Website 1+ mentions |
Crossbow (RRID:SCR_013306) | Crossbow | software resource | A scalable software pipeline for whole genome resequencing analysis. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19930550 DOI:10.1186/gb-2009-10-11-r134 |
biotools:crossbow, OMICS_00284 | https://bio.tools/crossbow | https://sources.debian.org/src/crossbow/ | SCR_013306 | SciCrunch Registry | 2026-10-24 12:47:03 | 5 | ||||||
|
INCLUSive Resource Report Resource Website 1+ mentions |
INCLUSive (RRID:SCR_013488) | INCLUSive | software resource | A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:12824346 | Acknowledgement requested | OMICS_00766, biotools:inclusive | https://bio.tools/inclusive | SCR_013488 | SciCrunch Registry | 2026-10-24 12:47:06 | 7 | ||||||
|
Alta-Cyclic Resource Report Resource Website |
Alta-Cyclic (RRID:SCR_013373) | Alta-Cyclic | software resource | An Illumina Genome-Analyzer (Solexa) base caller. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Cold Spring Harbor Laboratory |
OMICS_01149, biotools:alta-cyclic | https://bio.tools/alta-cyclic | SCR_013373 | SciCrunch Registry | 2026-10-24 12:47:04 | 0 | ||||||||
|
OsiriX Medical Imaging Software Resource Report Resource Website 1000+ mentions |
OsiriX Medical Imaging Software (RRID:SCR_013618) | data processing software, data visualization software, software application, software resource | :OsiriX is an image processing software dedicated to DICOM images (.dcm / .DCM extension) produced by medical equipment (MRI, CT, PET, PET-CT, ...) and confocal microscopy (LSM and BioRAD-PIC format). It can also read many other file formats: TIFF (8,16, 32 bits), JPEG, PDF, AVI, MPEG and Quicktime. It is fully compliant with the DICOM standard for image comunication and image file formats. OsiriX is able to receive images transferred by DICOM communication protocol from any PACS or medical imaging modality (STORE SCP - Service Class Provider, STORE SCU - Service Class User, and Query/Retrieve) . OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images: 2D Viewer, 3D Viewer, 4D Viewer (3D series with temporal dimension, for example: Cardiac-CT) and 5D Viewer (3D series with temporal and functional dimensions, for example: Cardiac-PET-CT). The 3D Viewer offers all modern rendering modes: Multiplanar reconstruction (MPR), Surface Rendering, Volume Rendering and Maximum Intensity Projection (MIP). All these modes support 4D data and are able to produce image fusion between two different series (for example: PET-CT). Osirix is at the same time a DICOM PACS workstation for medical imaging and an image processing software for medical research (radiology and nuclear imaging), functional imaging, 3D imaging, confocal microscopy and molecular imaging. : | bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:osirix, nif-0000-00340 | https://bio.tools/osirix | SCR_013618 | SciCrunch Registry | OsiriX | 2026-10-24 12:47:07 | 1444 | ||||||||
|
Pathway Tools Resource Report Resource Website 10+ mentions |
Pathway Tools (RRID:SCR_013786) | data management software, software application, software resource, software toolkit | A software application which supplies software tools to develop and maintain pathway/genome databases (PGDBs). These include the development of organism-specific databases, metabolic reconstruction and metabolic-flux modeling, scientific visualization and web publishing of organism-specific databases, analysis of gene-expression and metabolomics datasets, comparative genome and pathway analyses, and analysis of biological networks. | software application, bioinformatics, software, software system, pathway genome database, PGDB, bio.tools |
is used by: BioCyc is used by: EcoCyc is used by: MetaCyc is listed by: BioCyc is listed by: bio.tools is listed by: Debian is related to: BioCyc is related to: MetaCyc is related to: EcoCyc is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: BioCyc |
NIGMS GM077678; NIGMS GM080746; NIGMS GM75742 |
DOI:10.1093/bib/bbp043 | biotools:pathway_tools | http://bioinformatics.ai.sri.com/ptools/ptools-overview.html, https://bio.tools/pathway_tools | SCR_013786 | SciCrunch Registry | Pathway Tools Bioinformatics Software, Pathway Tools Software | 2026-10-24 12:47:10 | 25 | ||||||
|
Metabolomics Workbench Resource Report Resource Website 500+ mentions |
Metabolomics Workbench (RRID:SCR_013794) | MetWB | data or information resource, data repository, service resource, storage service resource | Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops. | repository, metabolomics, database, funding, training, protocol, bio.tools, FASEB list, DRKB |
is used by: NIH Heal Project is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases lists: NIH Metabolomics program lists: MetaCore lists: JMP lists: STATISTICA lists: Spotfire lists: Coordination of Standards in Metabolomics lists: MetaboLights lists: MetabolomeXchange lists: Metabolomics Society lists: Birmingham Metabolite Library lists: Glycan Mass Spectral Database (GMDB) lists: Mass Spectral Library lists: mzCloud lists: MetabolomeExpress lists: Spectral Database System (SDBS) lists: CTSgetR lists: Hierarchical Clustering lists: imDEV lists: Linear Discriminant Analysis lists: Principal Components Analysis lists: mwtabR lists: 3Omics lists: ACD/ NMR Processor lists: NIST Mass Spectrometry Data Center lists: Chemical Translation Service lists: Chenomx NMR Suite lists: DeviumWeb lists: MBRole lists: MetaMapR lists: MetaP lists: Metscape lists: SIMCA lists: TeachingDemos is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is listed by: re3data.org is listed by: DataCite has parent organization: University of California; California; USA is parent organization of: Metabolomics Workbench Metabolite Database |
NIDDK DK141185; NIH |
Free, Freely available | biotools:Metabolomics_Workbench, r3d100012314 | https://bio.tools/Metabolomics_Workbench, https://api.datacite.org/dois?prefix=10.21228 | SCR_013794 | SciCrunch Registry | Metabolomics Workbench, MetWB, UCSD Metabolomics Workbench, Metabolomics Workbench (MetWB) | 2026-10-24 12:47:10 | 666 | |||||
|
Membrane Protein Explorer Resource Report Resource Website 10+ mentions |
Membrane Protein Explorer (RRID:SCR_014077) | MPEx | data analysis software, data processing software, software application, software resource | Software which predicts topology and other features of membrane proteins through hydropathy plots based on thermodynamic and biological principles. This version of MPEx uses two types of hydropathy scales: Experiment-based whole-residue partitioning scales and experiment-based biological partitioning scales. The whole-residue partitioning scales predict the transmembrane (TM) segments of membrane proteins of known structure. The biological scale utilizes current knowledge of the code the Sec61 translocon to identify TM segments. MPEx is a Java program (not a Java applet) deployed using Java Web Start, which is part of the Java Runtime Environment. | membrane protein, hydropathy plot, topology, software, java, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at Irvine; California; USA |
PMID:19785006 | Available to the research community, Requires version 7 or higher of Java Runtime Environment | biotools:mpex | https://bio.tools/mpex | SCR_014077 | SciCrunch Registry | Membrane Protein Explorer (MPEx) | 2026-10-24 12:47:12 | 34 | |||||
|
Buccaneer Resource Report Resource Website 100+ mentions |
Buccaneer (RRID:SCR_014221) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software which performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target. The target distributions are generated by a simulation calculation using a known reference structure for which calculated phases are available. The success of the method is dependent on the features of the reference structure matching those of the unsolved work structure. For almost all cases, a single reference structure can be used, with modifications automatically applied to the reference structure to match its features to the work structure. | statistical chain tracing, alpha carbon position, sequence analysis software, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:16929101 | biotools:buccaneer | https://bio.tools/buccaneer | SCR_014221 | SciCrunch Registry | buccaneer - Statistical protein chain tracing | 2026-10-24 12:47:14 | 335 | |||||||
|
UALCAN Resource Report Resource Website 1000+ mentions |
UALCAN (RRID:SCR_015827) | data analysis software, data or information resource, data processing software, database, sequence analysis software, software application, software resource, web application | Web application and database for analyzing cancer transcriptome data. It also has applications is facilitating tumor subgroup gene expression and survival analyses. | tumor, gene expression, survival analysis, cancer transcriptome data, sequencing, biomarker, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:28732212 | Freely available | biotools:UALCAN | https://bio.tools/UALCAN | SCR_015827 | SciCrunch Registry | 2026-10-24 12:47:29 | 3128 | |||||||
|
circlncRNAnet Resource Report Resource Website 10+ mentions |
circlncRNAnet (RRID:SCR_015794) | data or information resource, data processing resource, database, software resource, web application | Web application for mapping functional networks of long or circular forms of non-coding RNAs. It supports the uploading and processing of user-defined NGS-based gene expression matrix data. | mapping, long form, circular form, non-coding rna, rna mapping, regulatory rna, ncRNA, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian requires: RStudio |
Freely available, Free, Available for download, Runs on Linux, Demo available, Tutorial available | biotools:circlncrnanet | https://github.com/smw1414/circlncRNAnet, https://bio.tools/circlncrnanet | SCR_015794 | SciCrunch Registry | 2026-10-24 12:47:30 | 33 | ||||||||
|
VaDiR Resource Report Resource Website 10+ mentions |
VaDiR (RRID:SCR_015797) | VaDiR | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource | Method for uncovering mutations from RNA sequencing datasets that could be useful in further functional analysis. It also allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing data sets. | rna-seq, somatic variant calling, ovarian cancer, cancer genomes transcriptome, orthogonal validation, genetic mutation, sequence variation analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Biostatistics and Informatics Shared Resource (BISR) ; Cancer Center Cancer Biology program ; Department of Defense Ovarian Cancer Research Program W81XWH-10-1-0386; NCI P30 CA168524; University of Kansas Endowment Association |
DOI:10.5524/100360 | Free, Available for download | biotools:vadir | ftp://penguin.genomics.cn/pub/10.5524/100001_101000/100360/, https://bio.tools/vadir | SCR_015797 | SciCrunch Registry | VaDiR: an integrated approach to Variant Detection in RNA | 2026-10-24 12:47:28 | 14 | ||||
|
Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | SciCrunch Registry | 2026-10-24 12:47:29 | 83 | ||||||
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SwissTree Resource Report Resource Website 1+ mentions |
SwissTree (RRID:SCR_015881) | data or information resource, data repository, data set, portal, project portal, service resource, storage service resource | Project that aims to provide a collection of Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure. | gene phylogeny, gene collection, gold standard, phylogenomic, database, genome analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Swiss National Science Foundation 150654; Swiss State Secretariat for Education ; Research and Innovation (SERI) |
Public, Free, Available for download | biotools:swisstree | https://bio.tools/swisstree | SCR_015881 | SciCrunch Registry | 2026-10-24 12:47:32 | 4 | |||||||
|
PhyD3 Resource Report Resource Website 50+ mentions |
PhyD3 (RRID:SCR_015892) | PhyD3 | data processing software, data visualization software, software application, software resource, web application | Web application that is a phylogenetic tree viewer based on d3.js. It was developed as an alternative to Archaeopteryx inspired by d3.phylogram.js. | javascript, visualization, toolkit, phylogeny, program, phylogenetic data, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28525531 | Open source, Demo available | biotools:phyd3 | https://github.com/vibbits/phyd3, https://bio.tools/phyd3 | SCR_015892 | SciCrunch Registry | 2026-10-24 12:47:29 | 57 | ||||||
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TFBS Resource Report Resource Website 10+ mentions |
TFBS (RRID:SCR_015774) | data analysis software, data processing software, software application, software resource | Perl software for transcription factor binding site detection and analysis. It implements classes for the representation of objects encountered in analysis of these protein-binding sites. | protein-binding, transcription factor, factor binding, binding site detection, transcription analysis, perl, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
PMID:12176838 DOI:10.1093/bioinformatics/18.8.1135 |
Free, Available for download, No longer in development | biotools:tfbs, OMICS_20526 | https://github.com/ComputationalRegulatoryGenomicsICL/TFBS, https://bio.tools/tfbs, https://sources.debian.org/src/libtfbs-perl/ | SCR_015774 | SciCrunch Registry | 2026-10-24 12:47:28 | 44 | |||||||
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Ariba Resource Report Resource Website 100+ mentions |
Ariba (RRID:SCR_015976) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling. | software, analysis, tool, sequence, antibiotic, resistance, assembly, local, mlst |
is listed by: Debian is listed by: OMICtools |
Biotechnology and Biological Sciences Research Council BB/M014088/1; Wellcome Trust 206194 |
PMID:29177089 DOI:10.1099/mgen.0.000131 |
Free, Available for download, Freely available | OMICS_17327 | https://sources.debian.org/src/artemis/ | SCR_015976 | SciCrunch Registry | 2026-10-24 12:47:30 | 220 | ||||||
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Atac Resource Report Resource Website 1000+ mentions |
Atac (RRID:SCR_015980) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences. | software, tool, DNA, sequence, analysis, aligning, genome, compare, mapping, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btr285 | Free, Freely available, Available for download | OMICS_29044, biotools:atac | https://bio.tools/atac, https://sources.debian.org/src/atac/ | SCR_015980 | SciCrunch Registry | 2026-10-24 12:47:33 | 1826 | |||||||
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BALLView Resource Report Resource Website 1+ mentions |
BALLView (RRID:SCR_015986) | data processing software, data visualization software, simulation software, software application, software resource, standalone software | Software for molecular visualization and modeling. It provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features. | molecular, modeling, visualization, application, computation, algorithm, library, bioinformatics |
is listed by: Debian is listed by: OMICtools |
Deutsche Forschungsgemeinschaft BIZ 1/1-3; BIZ 4/1-1 and LE 952/2-3 |
PMID:16332707 DOI:10.1093/bioinformatics/bti818 |
Free, Freely available, Free for download, Runs on Mac OS, Runs on Windows | OMICS_05049 | https://github.com/BALL-Project/ball/wiki/Tutorials, https://sources.debian.org/src/bamtools/ | SCR_015986 | SciCrunch Registry | BALL:Biochemical Algorithms Library, Biochemical Algorithms Library | 2026-10-24 12:47:30 | 4 | |||||
|
Axe Resource Report Resource Website 1+ mentions |
Axe (RRID:SCR_015984) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples. | software, tool, sequence, analysis, barcode, demultiplexing |
is listed by: Debian is listed by: OMICtools |
Free, Freely available, Available for download | OMICS_19788 | https://readthedocs.org/projects/axe-demultiplexer/, https://sources.debian.org/src/baitfisher/ | SCR_015984 | SciCrunch Registry | Axe-demultiplexer | 2026-10-24 12:47:30 | 1 |
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