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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MutationAssessor Resource Report Resource Website 500+ mentions |
MutationAssessor (RRID:SCR_005762) | mutationassessor.org | analysis service resource, data analysis service, production service resource, service resource | A web server that predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on a large set (51k) of disease associated (OMIM) and polymorphic variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | cancer, protein, mutation, function, amino-acid, substitution |
is listed by: OMICtools is listed by: SoftCite |
PMID:21727090 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00134, nlx_149228 | SCR_005762 | SciCrunch Registry | MutationAssessor - functional impact of protein mutations, MutationAssessor - functional impact of mutations, mutationassessor.org - functional impact of protein mutations | 2026-10-31 12:20:07 | 693 | ||||||
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mitopred Resource Report Resource Website 1+ mentions |
mitopred (RRID:SCR_006135) | MITOPRED | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It predicts nuclear-encoded mitochondrial proteins from all eukaryotic species including plants. Prediction is based on the occurrence patterns of Pfam domains (version 16.0) in different cellular locations, amino acid composition and pI value differences between mitochondrial and non-mitochondrial locations. Additionally, you may download MITOPRED predictions for complete proteomes. Re-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. The Mitopred algorithm works based on the differences in the Pfam domain occurrence patters and amino acid composition differences in different cellular compartments. Location specific Pfam domains have been determined from the entire eukaryotic set of Swissprot database. Similarly, differences in the amino acid composition between mitochondrial and non-mitochondrial sequences were pre-calculated. This information is used to calculate location-specific amino acid weights that are used to calculate amino acid score. Similarly, pI average values of the N-terminal 25 residues in different cellular location were also determined. This knowledge-base is accessed by the program during execution. | yeast, c. elegans, drosophila, mouse, human, arabidopsis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University at Albany; New York; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mitopred, nif-0000-03956, BioTools:mitopred | https://bio.tools/mitopred, https://bio.tools/mitopred, https://bio.tools/mitopred | SCR_006135 | SciCrunch Registry | A genome-scale method for predicting mitochondrial proteins | 2026-10-31 12:20:10 | 7 | ||||||
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riskRegression Resource Report Resource Website 10+ mentions |
riskRegression (RRID:SCR_024424) | software resource, software toolkit | Software R package provides risk regression models and prediction scores for survival analysis with competing risks. | risk prediction, risk regression models, prediction scores, survival analysis, competing risks, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/tagteam/riskRegression | SCR_024424 | SciCrunch Registry | 2026-10-31 12:19:37 | 15 | |||||||||
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RapGreen Resource Report Resource Website 1+ mentions |
RapGreen (RRID:SCR_024426) | PMID:34568824 | software resource, software toolkit | Software phylogenetic tree analysis package. Phylogenetic tree management, exploration and display package. | Phylogenetic tree management, phylogenetic tree analysis, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/SouthGreenPlatform/rap-green/wiki, http://southgreenplatform.github.io/rap-green/ | SCR_024426 | SciCrunch Registry | 2026-10-31 12:19:39 | 1 | ||||||||
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ROCit Resource Report Resource Website 1+ mentions |
ROCit (RRID:SCR_024420) | software resource, software toolkit | Software R package for assessing overall diagnostic ability of binary classifier. Used to evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot. | assessing overall diagnostic ability of binary classifier, evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024420 | SciCrunch Registry | Receiver Operating Characteristic it | 2026-10-31 12:19:41 | 1 | |||||||||
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Rgdal Resource Report Resource Website 1+ mentions |
Rgdal (RRID:SCR_024422) | software resource, software toolkit | Software R package provides bindings for the Geospatial Data Abstraction Library. Translator library for raster and vector geospatial data formats. | Translator library, geospatial data formats, Geospatial Data Abstraction Library bindings, | is listed by: SoftCite | Free, Available for download, Freely available | https://r-forge.r-project.org/projects/rgdal/ | SCR_024422 | SciCrunch Registry | , R geospatial data abstraction library, rgdal | 2026-10-31 12:19:37 | 6 | ||||||||
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survivalROC Resource Report Resource Website 10+ mentions |
survivalROC (RRID:SCR_024415) | software resource, software toolkit | Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data. | compute time dependent Receiver Operating Characteristic curve, censored survival data, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024415 | SciCrunch Registry | survival Receiver Operating Characteristic | 2026-10-31 12:19:37 | 23 | |||||||||
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ggridges Resource Report Resource Website 1+ mentions |
ggridges (RRID:SCR_024511) | software resource, software toolkit | Software R package enables creation of Ridgeline plots in 'ggplot2' | creation of Ridgeline plots in 'ggplot2', | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/wilkelab/ggridges | SCR_024511 | SciCrunch Registry | 2026-10-31 12:19:38 | 8 | |||||||||
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gamm4 Resource Report Resource Website 1+ mentions |
gamm4 (RRID:SCR_024507) | software resource, software toolkit | Software R package to estimate generalized additive mixed models. | estimate generalized additive mixed models, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024507 | SciCrunch Registry | 2026-10-31 12:19:38 | 4 | ||||||||||
|
Inference of CRISPR Edits Resource Report Resource Website 100+ mentions |
Inference of CRISPR Edits (RRID:SCR_024508) | ICE | analysis service resource, production service resource, service resource, software resource | Software tool that offers analysis of CRISPR editing data. Used for inference of CRISPR edits from Sanger trace data. | analysis of CRISPR editing data, CRISPR editing analysis, | is listed by: SoftCite | PMID:35119294 | Free, Freely available | https://github.com/synthego-open/ice#ref2 | SCR_024508 | SciCrunch Registry | Synthego Inference of CRISPR Edits | 2026-10-31 12:19:37 | 103 | ||||||
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Optimization Toolbox Resource Report Resource Website 1+ mentions |
Optimization Toolbox (RRID:SCR_024486) | software resource, software toolkit | Software package provides functions for finding parameters that minimize or maximize objectives while satisfying constraints. Toolbox includes solvers for linear programming, mixed integer linear programming, quadratic programming, second order cone programming, nonlinear programming, constrained linear least squares, nonlinear least squares, nonlinear equations. | Mathworks, finding parameters, minimize or maximize objectives, linear programming solver, mixed integer linear programming solver, quadratic programming solver, second order cone programming solver, nonlinear programming solver, constrained linear least squares solver, nonlinear least squares solver, nonlinear equations solver, | is listed by: SoftCite | Restricted | SCR_024486 | SciCrunch Registry | 2026-10-31 12:19:39 | 1 | ||||||||||
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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 | 2026-10-31 12:19:38 | 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 | 2026-10-31 12:19:41 | 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 | 2026-10-31 12:19:38 | 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 | 2026-10-31 12:19:42 | 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 | 2026-10-31 12:19:43 | 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 | 2026-10-31 12:19:56 | 6113 | |||||||
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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 | 2026-10-31 12:18:31 | 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 | 2026-10-31 12:18:30 | 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 | 2026-10-31 12:18:33 | 45 |
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