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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
BLASR Resource Report Resource Website 10+ mentions Discontinued |
BLASR (RRID:SCR_000764) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Proovread |
PMID:22988817 DOI:10.1186/1471-2105-13-23 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:blasr, OMICS_05134 | https://bio.tools/blasr https://sources.debian.org/src/blasr/ |
SCR_000764 | Basic Local Alignment with Successive Refinement, BLASR: The PacBio long read aligner | 2026-02-07 02:05:23 | 15 | ||||||
|
ADEGENET Resource Report Resource Website 10+ mentions Issue |
ADEGENET (RRID:SCR_000825) | ADEGENET | software resource, software application | Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic, r |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
PMID:21926124 PMID:18397895 DOI:10.1093/bioinformatics/btn129 |
Free, Available for download, Freely available | nlx_153996, nlx_154580, OMICS_11078, SCR_007239 | http://adegenet.r-forge.r-project.org/ https://sources.debian.org/src/r-cran-adegenet/ |
SCR_000825 | R/ADEGENET | 2026-02-10 09:54:24 | 20 | |||||
|
FlashPCA Resource Report Resource Website 10+ mentions Issue |
FlashPCA (RRID:SCR_021680) | software resource, software application, data processing software, data analysis software | Software tool as fast principal component analysis of large scale genome wide data. FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data. FlashPCA2 used for principal component analysis of biobank scale genotype datasets. | Principal component analysis, large scale genome wide data, single nucleotide polymorphism data, biobank scale genotype datasets | DOI:10.1093/bioinformatics/btx299 DOI:10.1371/journal.pone.0093766 |
Free, Available for download, Freely available | SCR_021680 | FlashPCA2 | 2026-02-11 11:00:12 | 33 | |||||||||
|
SPM Resource Report Resource Website 5000+ mentions Issue |
SPM (RRID:SCR_007037) | SPM | software application, image analysis software, software resource, data analysis software, data processing software | 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 | 2026-02-11 10:57:28 | 8694 | |||||
|
GenAlEx Resource Report Resource Website 50+ mentions Issue |
GenAlEx (RRID:SCR_021102) | software application, software resource, software toolkit, data analysis software, data processing software | Software tool as cross platform package for population genetic analyses that runs within Microsoft Excel. Offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences.Originally developed as teaching tool to facilitate teaching population genetic analysis at graduate level. | population genetic analyses, Microsoft Excel, diploid codominant analysis, haploid genetic loci, binary genetic loci, DNA sequences analysis | PMID:22820204 | Free, Available for download, Freely available | SCR_021102 | GenAlEx 6.5, Genetic Analysis in Excel | 2026-02-11 11:00:01 | 75 | |||||||||
|
Willoughby–Hoye Python Scripts A-D Resource Report Resource Website 1+ mentions Issue |
Willoughby–Hoye Python Scripts A-D (RRID:SCR_017562) | software resource, software application, data processing software, data analysis software | Software tool as scripts for calculating NMR chemical shifts. Warning - this group of Python scripts used to process NMR data, described in Willoughby et al, 2014, has been found to contain bug. Please see PMID:31591889. | Python, NMR, script, caluclating, chemical, shift, data | NIA R01 AG039468 | PMID:24556787 PMID:31591889 |
Free, Freely available | SCR_017562 | 2026-02-11 10:59:38 | 1 | |||||||||
|
PLINK Resource Report Resource Website 10000+ mentions Issue |
PLINK (RRID:SCR_001757) | software application, software resource, software toolkit, data analysis software, data processing software | Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software. | gene, genetic, genomic, genotype, phenotype, copy number variant, whole-genome association, population, linkage analysis, whole-genome association study, data management, summary statistics, population stratification, association analysis, identity-by-descent estimation |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Whap is related to: PLINK/SEQ is related to: Haploview is related to: MendelIHT.jl |
PMID:17701901 DOI:10.1086/519795 |
Free, Available for download, Freely Available | nlx_154200, OMICS_00206, SCR_021271 | https://zzz.bwh.harvard.edu/plink/ https://www.cog-genomics.org/plink/1.9/general_usage#cite https://sources.debian.org/src/plink/ |
http://pngu.mgh.harvard.edu/~purcell/plink/ | SCR_001757 | PLINK 1.9, PLINK/SEQ, plink - Whole genome association analysis toolset | 2026-02-11 10:56:18 | 15344 | |||||
|
ClustVis Resource Report Resource Website 500+ mentions Issue |
ClustVis (RRID:SCR_017133) | production service resource, software resource, web service, data access protocol, data analysis service, service resource, analysis service resource | Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps. | visualizing, clustering, multivariate, data, principal, component, analysis, plot, heatmap, bio.tools |
uses: Shiny uses: ggplot2 uses: pheatmap uses: RColorBrewer uses: FactoMineR is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing has parent organization: University of Tartu; Tartu; Estonia |
Innovative Medicines Initiative Joint Undertaking ; European Union Seventh Framework Programme ; European Federation of Pharmaceutical Industries and Associations ; European Regional Development Fund ; Estonian Research Council ; European Commission ; EFPIA |
PMID:25969447 | biotools:clustvis, OMICS_08539 | https://github.com/taunometsalu/ClustVis https://bio.tools/clustvis |
SCR_017133 | 2026-02-11 10:59:34 | 798 | |||||||
|
Eigensoft Resource Report Resource Website 1000+ mentions Issue |
Eigensoft (RRID:SCR_004965) | EIGENSOFT | software resource, software toolkit | EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction. | population genetics, genetics, stratification, variation |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: Harvard Medical School; Massachusetts; USA |
PMID:17194218 DOI:10.1038/ng1847 |
OMICS_07868, nlx_93059 | https://sources.debian.org/src/eigensoft/ | http://genepath.med.harvard.edu/~reich/Software.htm | SCR_004965 | EIGENSOFT Software | 2026-02-11 10:57:00 | 1225 | |||||
|
pcadapt Resource Report Resource Website 1+ mentions Issue |
pcadapt (RRID:SCR_022019) | software resource, software toolkit | Software R package for fast Principal Component Analysis for outlier detection.Used to detect genetic markers involved in biological adaptation. Performs genome scans for selection based on principal component analysis. | PCA, genome scans, Principal Component Analysis, outlier detection, detect genetic markers involved in biological adaptation | LabEx PERSYVAL Lab ; ANR AGRHUM |
DOI:10.1111/1755-0998.12592 PMID:32343802 PMID:27601374 |
Free, Available for download, Freely available | https://github.com/bcm-uga/pcadapt | SCR_022019 | 2026-02-11 11:00:14 | 3 |
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