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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 | , Copynumber Karyotyping of Aneuploid Tumors | 2026-09-05 06:31:08 | 84 | ||||||||
|
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 | Class Intervals | 2026-09-05 06:31:09 | 2 | ||||||||
|
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 | 2026-09-05 06:31:09 | 1 | |||||||||
|
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 | blastp suite, Standard Protein BLAST | 2026-09-05 06:31:12 | 293 | ||||||||
|
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 | PREFAB - Protein Reference Alignment Benchmark, Protein Reference Alignment Benchmark | 2026-09-05 06:31:12 | 1 | ||||||
|
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 | Statistical Parametric Mapping, SPM5, SPM2, SPM12, Statistical Parametric Mapping Software, SPM99, SPM8, SPM, SPM96 | 2026-09-05 06:30:00 | 8748 | |||||
|
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 | MUltiple Sequence Comparison by Log- Expectation | 2026-09-05 06:30:03 | 17169 | ||||||
|
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 | 2026-09-05 06:30:03 | 187 | |||||||||
|
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 | 2026-09-05 06:30:06 | 1661 | ||||||
|
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 | , GeneMapper Software 5, GeneMapper Software 6, GeneMapper Software | 2026-09-05 06:30:05 | 5354 | |||||||
|
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 | NONMEM 7.4, NONMEM 7, Nonlinear mixed effects modelling software, NONMEM 7.2, NONlinear Mixed Effects Modeling software, population analysis | 2026-09-05 06:30:08 | 45 | ||||||||
|
SignalP Resource Report Resource Website 10000+ mentions |
SignalP (RRID:SCR_015644) | software resource, web application | Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. | prediction, signal peptide, cleavage site, amino acid, sequence, artificial neural network |
is listed by: SoftCite has parent organization: DTU Center for Biological Sequence Analysis |
PMID:28451972 | Freely available, Acknowledgment requested, Free, Available for download, Runs on Windows, Runs on Mac OS | SCR_015644 | 2026-09-05 06:30:18 | 10033 | |||||||||
|
MRIcron Resource Report Resource Website 1000+ mentions |
MRIcron (RRID:SCR_002403) | MRIcron | data processing software, data visualization software, software application, software resource | Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. | NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools |
is used by: XFSL: An FSL toolbox is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: neurodebian is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Colour maps for brain imaging has parent organization: University of South Carolina; South Carolina; USA |
PMID:17583985 PMID:11568431 |
BSD License | biotools:MRIcron, nif-0000-00122 | https://sources.debian.org/src/mricron/, http://www.mccauslandcenter.sc.edu/mricro/, http://www.nitrc.org/projects/mricron, http://neuro.debian.net/pkgs/mricron.html, https://bio.tools/MRIcron | SCR_002403 | mricron - magnetic resonance image conversion viewing and analysis | 2026-09-05 06:30:20 | 2312 | |||||
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QuantPrime Resource Report Resource Website 100+ mentions |
QuantPrime (RRID:SCR_015498) | software resource, web application | Fully automated tool for primer pair design in small- to large-scale real-time reverse transcription qPCR analyses. It offers design and specificity checking with highly customizable parameters and is available for use with publicly available eukaryotic transcriptomes. | primer design, primer pair design, rt-qpcr, reverse transcription qpcr | is listed by: SoftCite | DOI:10.1186/1471-2105-9-465 | Acknowledgement requested, Available as a web application, Available as a desktop application | SCR_015498 | 2026-09-05 06:30:21 | 162 | |||||||||
|
ModFit LT Resource Report Resource Website 100+ mentions |
ModFit LT (RRID:SCR_016106) | data processing software, data visualization software, software application, software resource | Modeling software for flow cytometry histograms. Models for cell-tracking dye studies and synchronized cell lines are built right into the software. | flow, cytometry, histogram, model, graph, cell, tracking, dye, cell line | is listed by: SoftCite | Commercially available, Available for purchase, Trial available | SCR_016106 | Verity Software House ModFit LT | 2026-09-05 06:30:21 | 154 | |||||||||
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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 | 2026-09-05 06:30:31 | 106 | |||||||
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PyWavelets Resource Report Resource Website 10+ mentions |
PyWavelets (RRID:SCR_024421) | data analysis software, data processing software, software application, software resource | Software Python package for wavelet analysis. | Python, wavelet analysis, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024421 | 2026-09-05 06:30:30 | 17 | ||||||||||
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ProteinPilot Resource Report Resource Website 100+ mentions |
ProteinPilot (RRID:SCR_024414) | data analysis software, data processing software, software application, software resource | Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems. | protein identification, protein expression analysis, post translational modification search, | is listed by: SoftCite | Restricted | https://sciex.com/content/dam/SCIEX/pdf/posters/ProteinPilot-Software-Overview.pdf | SCR_024414 | 2026-09-05 06:30:30 | 265 | |||||||||
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pRRophetic Resource Report Resource Website 10+ mentions |
pRRophetic (RRID:SCR_024417) | simulation software, software application, software resource | Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data, | clinical chemotherapeutic response prediction, tumor gene expression levels, predict phenotypes, | is listed by: SoftCite | U01GM61393 ; GM089941 ; CA139278 ; University of Chicago ; UL1RR024999 |
PMID:25229481 | Free, Available for download, Freely available | SCR_024417 | 2026-09-05 06:30:30 | 33 | ||||||||
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VSEARCH Resource Report Resource Website 1000+ mentions |
VSEARCH (RRID:SCR_024494) | data analysis software, data processing software, software application, software resource | Software versatile open source tool for metagenomics. Used for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. | processing and preparing metagenomics, genomics and population genomics, nucleotide sequence data, | is listed by: SoftCite | PMID:27781170 | Free, Available for download, Freely available | SCR_024494 | 2026-09-05 06:30:31 | 1553 |
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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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