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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CopyKAT Resource Report Resource Website 50+ mentions |
CopyKAT (RRID:SCR_024512) | software resource, software toolkit | Software R package to estimate genomic copy number profiles at average genomic resolution of 5 Mb from read depth in high throughput single cell RNA sequencing data.Used for inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data. | Inference of genomic copy number and subclonal structure of human tumors, high throughput single cell RNAseq data, | is listed by: SoftCite | PMID:33462507 | Free, Available for download, Freely available | SCR_024512 | SciCrunch Registry | , Copynumber Karyotyping of Aneuploid Tumors | 2026-11-07 12:01:52 | 84 | ||||||||
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classInt Resource Report Resource Website 1+ mentions |
classInt (RRID:SCR_024515) | software resource, software toolkit | Software R package for choosing univariate class intervals for mapping or other graphics purposes. | choosing univariate class intervals, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/r-spatial/classInt/ | SCR_024515 | SciCrunch Registry | Class Intervals | 2026-11-07 12:02:00 | 2 | ||||||||
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mitml Resource Report Resource Website 1+ mentions |
mitml (RRID:SCR_024516) | software resource, software toolkit | Software R package for multiple imputation of missing data in multilevel modeling. | multiple imputation of missing data in multilevel modeling, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/simongrund1/mitml | SCR_024516 | SciCrunch Registry | 2026-11-07 12:01:52 | 1 | |||||||||
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BLASTP Resource Report Resource Website 100+ mentions |
BLASTP (RRID:SCR_001010) | analysis service resource, data analysis service, production service resource, service resource | Data analysis service whose programs search protein databases using a protein query. The algorithms used include blastp, psi-blast, phi-blast, and delta-blast. | blast, basic local alignment search tool, protein alignment, protein blast, data analysis service, protein |
is used by: Open Reading Frame Finder is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI |
Freely available, Acknowledgement requested | OMICS_00991 | SCR_001010 | SciCrunch Registry | blastp suite, Standard Protein BLAST | 2026-11-07 12:01:55 | 293 | ||||||||
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PREFAB Resource Report Resource Website 1+ mentions |
PREFAB (RRID:SCR_001009) | PREFAB | data or information resource, database | Downloadable data designed for testing multiple sequence alignment methods. | database, downloadable data, sequence alignment, sequence alignment method |
is listed by: OMICtools is listed by: SoftCite is related to: MUSCLE |
PMID:15034147 | Free, Available for download, Freely available | OMICS_00984 | SCR_001009 | SciCrunch Registry | PREFAB - Protein Reference Alignment Benchmark, Protein Reference Alignment Benchmark | 2026-11-07 12:01:56 | 1 | ||||||
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Primer-BLAST Resource Report Resource Website 5000+ mentions |
Primer-BLAST (RRID:SCR_003095) | Primer-BLAST | analysis service resource, data analysis service, production service resource, service resource | A tool to design target-specific primers for polymerase chain reaction (PCR). It uses Primer3 to design PCR primers and then uses BLAST and global alignment algorithm to screen primers against user-selected database in order to avoid primer pairs (all combinations including forward-reverse primer pair, forward-forward as well as reverse-reverse pairs) that can cause non-specific amplifications. | primer, blast, pcr target, polymerase chain reaction, primer design |
is listed by: OMICtools is listed by: SoftCite is related to: Primer3 has parent organization: NCBI |
PMID:22708584 | Free, Freely available | OMICS_02343 | SCR_003095 | SciCrunch Registry | 2026-11-07 12:02:31 | 6113 | |||||||
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TreeBASE Resource Report Resource Website 500+ mentions |
TreeBASE (RRID:SCR_005688) | TreeBASE | data or information resource, data repository, database, service resource, storage service resource | Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but will not be available to the public until they have passed peer review. | taxonomy, matrix, tree, topology, phylogeography, cladistic analysis, amino acid sequence, animal behavior, morphology, nucleotide sequence, genetics, dna, phylogeny, evolution, gene, population, web service, FASEB list |
is listed by: re3data.org is listed by: SoftCite has parent organization: NESCent - National Evolutionary Synthesis Center |
NSF DEB 9318325; NSF EF 0331654 |
Public, The community can contribute to this resource | r3d100010170, nif-0000-03587 | https://doi.org/10.17616/R3DK58 | SCR_005688 | SciCrunch Registry | TreeBASE - A Database of Phylogenetic Knowledge | 2026-11-07 12:00:13 | 813 | |||||
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SPM Resource Report Resource Website 5000+ mentions Issue |
SPM (RRID:SCR_007037) | SPM | data analysis software, data processing software, image analysis software, software application, software resource | Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG. | analysis, brain, imaging, data, sequence, fMRI, PET, SPECT, EEG, MEG, bio.tools |
uses: Neuroimaging Data Model uses: imcalc: SPM batch image calculator is used by: rsfMRI_fconn calculation is used by: Automatic Analysis is used by: auto_acpc_reorient is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: SoftCite is affiliated with: Clinical Toolbox for SPM is affiliated with: Statistical non-Parametric Mapping is related to: WFU Biological Parametric Mapping Toolbox is related to: vis: SPM Visualized Statistics toolbox is related to: LEAD-DBS is related to: CCHMC Pediatric Brain Templates is related to: IBMA toolbox is related to: ArtRepair for robust fMRI is related to: ASL data processing tool box is related to: BrainVISA / Anatomist is related to: MRIcro Software is related to: xjView: A Viewing Program For SPM is related to: BrainMagix SPM Viewer is related to: MarsBaR region of interest toolbox for SPM is related to: NIRS-SPM is related to: SPM SS - fMRI functional localizers is related to: Wisconsin White Matter Hyperintensities Segmentation Toolbox is related to: Dementia-specific FDG PET Template for SPM analyses is related to: SPM Anatomy Toolbox is related to: MIPAV: Medical Image Processing and Visualization is related to: MATLAB is related to: hMRI-toolbox is related to: Sandwich Estimator Toolbox has parent organization: University College London; London; United Kingdom is required by: MRTool provides: TSDiffAna has plug in: ICN_Atlas works with: UManitoba - JHU Functionally Defined Human White Matter Atlas works with: NIAG Addiction Data works with: ICN_Atlas works with: spm_auto_reorient_coregister works with: Computational Anatomy Toolbox for SPM works with: FieldTrip works with: POAS4SPM |
Free, Available for download, Freely available | biotools:SPM | https://github.com/spm/spm12, https://bio.tools/SPM | https://www.fil.ion.ucl.ac.uk/spm/ | SCR_007037 | SciCrunch Registry | Statistical Parametric Mapping, SPM5, SPM2, SPM12, Statistical Parametric Mapping Software, SPM99, SPM8, SPM, SPM96 | 2026-11-07 12:00:37 | 8748 | |||||
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MUSCLE Resource Report Resource Website 10000+ mentions |
MUSCLE (RRID:SCR_011812) | MUSCLE | alignment software, analysis service resource, data analysis service, data analysis software, data processing software, image analysis software, production service resource, service resource, software application, software resource | Multiple sequence alignment method with reduced time and space complexity.Multiple sequence alignment with high accuracy and high throughput. Data analysis service for multiple sequence comparison by log- expectation. | bio.tools |
is used by: TranslatorX is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: PREFAB has parent organization: European Bioinformatics Institute |
PMID:15034147 PMID:15318951 DOI:10.1093/nar/gkh340 |
biotools:muscle, OMICS_00982 | https://bio.tools/muscle, http://www.drive5.com/muscle/, https://www.drive5.com/muscle/manual/, https://www.drive5, http://bioconductor.org/packages/release/bioc/html/muscle.html.com/muscle/manual/install.html, https://sources.debian.org/src/muscle/ | SCR_011812 | SciCrunch Registry | MUltiple Sequence Comparison by Log- Expectation | 2026-11-07 12:00:49 | 17169 | ||||||
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CLC Genomics Workbench Resource Report Resource Website 100+ mentions |
CLC Genomics Workbench (RRID:SCR_011853) | data analysis software, data processing software, data visualization software, software application, software resource | Commercially available software for visualization and analysis of next generation sequencing data. Used for viewing, exploring, and sharing of NGS analysis results. Complete toolkit for genomics, transcriptomics, epigenomics, and metagenomics in one program. | ngs, next, generation, sequencing, gene, rna, visualisation, analysis |
is listed by: OMICtools is listed by: SoftCite works with: CLC Genomics Server |
Restricted | SCR_016245, OMICS_01124 | SCR_011853 | SciCrunch Registry | 2026-11-07 12:00:17 | 187 | |||||||||
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Gwyddion Resource Report Resource Website 1000+ mentions |
Gwyddion (RRID:SCR_015583) | data analysis software, data processing software, software application, software resource | Modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for the analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of SPM data formats. However, it can be used for general height field and (greyscale) image processing, for instance for the analysis of profilometry data or thickness maps from imaging spectrophotometry. | spm data analysis, spm data visualization, height field analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Czech Metrology Institute Department of Nanometrology | DOI:10.2478/s11534-011-0096-2 | Open source | OMICS_07548 | https://sources.debian.org/src/gwyddion/ | SCR_015583 | SciCrunch Registry | 2026-11-07 12:00:51 | 1661 | ||||||
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GeneMapper Resource Report Resource Website 5000+ mentions |
GeneMapper (RRID:SCR_014290) | data analysis software, data processing software, sequence analysis software, software application, software resource | Genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. GeneMapper specializes in multiapplication functionality, including amplified fragment length polymorphism, loss of heterozygosity, microsatellite, and SNP genotyping analysis. The software provides remote auto-analysis and command line operation, and allows for multiuser, client-server deployment. | genotyping software, sequence analysis software, multiplication functionality, dna sizing, allele call, electrophoresis genotyping system | is listed by: SoftCite | Restricted | https://www.thermofisher.com/order/catalog/product/de/en/4370784, https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2F4476603A.pdf, | https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600798&tab=DetailInfo | SCR_014290 | SciCrunch Registry | , GeneMapper Software 5, GeneMapper Software 6, GeneMapper Software | 2026-11-07 12:00:50 | 5354 | |||||||
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NONMEM Resource Report Resource Website 10+ mentions |
NONMEM (RRID:SCR_016986) | Nonmem | data analysis software, data processing software, simulation software, software application, software resource | Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions. | nonlinear, mixed, effect, modeling, pharmacokinetic, pharmacodynamic, analysis, data | is listed by: SoftCite | Commercially available | SCR_016986 | SciCrunch Registry | NONMEM 7.4, NONMEM 7, Nonlinear mixed effects modelling software, NONMEM 7.2, NONlinear Mixed Effects Modeling software, population analysis | 2026-11-07 12:00:52 | 45 | ||||||||
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BoxPlotR Resource Report Resource Website 100+ mentions |
BoxPlotR (RRID:SCR_015629) | data processing software, data visualization software, software application, software resource, web application | Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox. | Box plot generation, customized box plot, data, plot, analysis |
is listed by: SoftCite is related to: PlotsOfData is related to: vioplot |
ERC ; Genome Québec International Recruitment Award ; Wellcome Trust ; WTCCB |
PMID:24481215 | Free, Available for download, Freely available | SCR_018327 | https://github.com/VizWizard/BoxPlotR.shiny | SCR_015629 | SciCrunch Registry | 2026-11-07 11:58:28 | 370 | ||||||
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oligo Resource Report Resource Website 1000+ mentions |
oligo (RRID:SCR_015729) | data analysis software, data processing software, software application, software resource, source code | Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). | oligonucleotide, microarray gene expression, r, oligonucleotide array, snp, gene expression, probe-level, affymetrix array, cel file, and nimblegen array, xys file, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
CAPES (Coordenação de Aprimoramento Pessoal de Nível Superior) ; NCRR R01RR021967; NHGRI P41HG004059 |
PMID:20688976 | Free, Available for download, Runs on Mac OS, Runs on Windows | biotools:oligo | https://bio.tools/oligo | SCR_015729 | SciCrunch Registry | oligo package | 2026-11-07 11:58:14 | 1808 | |||||
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GeneMarker Resource Report Resource Website 1000+ mentions |
GeneMarker (RRID:SCR_015661) | data analysis software, data processing software, software application, software resource | Genotype analysis software which enhances the speed, accuracy, and ease of analysis. The software is an alternative to Applied BioSystems Genotyper®, GeneScan®, and other genotype analysis software. | genotype, gene analysis | is listed by: SoftCite | Commercially available, Trial available, Runs on Mac OS, Runs on Windows, Runs on Linux | SCR_015661 | SciCrunch Registry | GeneMarker: The Biologist Friendly Software | 2026-11-07 11:58:13 | 1577 | |||||||||
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Phobius Resource Report Resource Website 500+ mentions |
Phobius (RRID:SCR_015643) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web application for combined transmembrane topology and signal peptide prediction. Used for whole genome annotation of signal peptides and transmembrane regions. Predictor is based on hidden Markov model (HMM) that models different sequence regions of signal peptide and different regions of transmembrane protein in series of interconnected states. | Signal peptide prediction, whole genome annotation, transmembrane region, protein prediction, transmembrane topology, signal peptide, fasta, hidden markov model | is listed by: SoftCite | PMID:15111065 PMID:30976793 |
Freely Available, Free, Available for download | SCR_018767 | http://phobius.binf.ku.dk/, https://www.ebi.ac.uk/Tools/pfa/phobius/ | SCR_015643 | SciCrunch Registry | PHOBIUS | 2026-11-07 11:58:28 | 553 | ||||||
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Genesis Resource Report Resource Website 1000+ mentions |
Genesis (RRID:SCR_015775) | data analysis software, data processing software, data visualization software, software application, software resource | Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments. | cluster analysis, microarray data, java, gene expression, visualization, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:11836235 | Free for academic use, Free for non-profits, Available for download, Runs on Windows, Runs on Mac OS, Runs on Linux | biotools:genesis_microarray | https://bio.tools/genesis_microarray | SCR_015775 | SciCrunch Registry | Genesis: Cluster analysis of microarray data | 2026-11-07 11:58:15 | 1029 | ||||||
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Gblocks Resource Report Resource Website 1000+ mentions |
Gblocks (RRID:SCR_015945) | software application, software resource, standalone software, web application | Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | position, dna, protein, align, alignment, phylogenetic, analysis, block, ansi c, deletion, removal | is listed by: SoftCite | Desarrollo e Innovación Tecnológica ; Fundación BBVA ; Plan Nacional de Investigación Científica BIO2002-04426-C02-02 |
PMID:10742046 PMID:17654362 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015945 | SciCrunch Registry | 2026-11-07 11:58:30 | 2043 | ||||||||
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AMBER Resource Report Resource Website 1000+ mentions |
AMBER (RRID:SCR_016151) | AMBER | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. | binning, metagenomics, benchmarking, biobox, evaluation, comparison, reconstruction, metric, |
is used by: CHARMM-GUI is listed by: SoftCite |
DOI:10.1101/239582 | Free, Available for download | SCR_016151 | SciCrunch Registry | AMBER: Assessment of Metagenome BinnERs | 2026-11-07 11:58:22 | 2205 |
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