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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-02-11 11:00:50 | 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 | Receiver Operating Characteristic it | 2026-02-11 11:00:46 | 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 | , R geospatial data abstraction library, rgdal | 2026-02-11 11:00:50 | 3 | ||||||||
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survivalROC Resource Report Resource Website 1+ 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 | survival Receiver Operating Characteristic | 2026-02-11 11:00:46 | 9 | |||||||||
|
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 | 2026-02-11 11:00:50 | 5 | |||||||||
|
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 | 2026-02-11 11:00:50 | 3 | ||||||||||
|
Inference of CRISPR Edits Resource Report Resource Website 50+ mentions |
Inference of CRISPR Edits (RRID:SCR_024508) | ICE | software resource, service resource, production service resource, analysis service 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 | Synthego Inference of CRISPR Edits | 2026-02-11 11:00:52 | 64 | ||||||
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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 | 2026-02-11 11:00:45 | 1 | ||||||||||
|
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 | 2026-02-11 11:00:52 | 65 | ||||||||
|
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 | 2026-02-11 11:00:50 | 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 | 2026-02-11 11:00:52 | 1 | |||||||||
|
BLASTP Resource Report Resource Website 100+ mentions |
BLASTP (RRID:SCR_001010) | data analysis service, service resource, production service resource, analysis 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 | 2026-02-11 10:56:09 | 286 | ||||||||
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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 | PREFAB - Protein Reference Alignment Benchmark, Protein Reference Alignment Benchmark | 2026-02-11 10:56:09 | 1 | ||||||
|
Primer-BLAST Resource Report Resource Website 5000+ mentions |
Primer-BLAST (RRID:SCR_003095) | Primer-BLAST | data analysis service, service resource, production service resource, analysis 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 | 2026-02-11 10:56:41 | 5498 | |||||||
|
Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | software resource, software application, data processing software, data analysis software | Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. | Data matrice analysis, data matrice modification, phyloinformatics, phylogenetic tree, alignment, molecular data manipulation, data analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: NCBI |
NSF Cyberinfrastructure for Phylogenetic Research EF 0331654 | PMID:18227120 | Free, Freely available | OMICS_21687 | https://sources.debian.org/src/phyutility/ | SCR_018545 | 2026-02-11 10:59:49 | 42 | ||||||
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SEDFIT Resource Report Resource Website 10+ mentions |
SEDFIT (RRID:SCR_018365) | software resource, software application, data processing software, data analysis software | Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly. | Analytical ultracentrifugation, biophysical analysis, macromolecular assembly, data, analysis, National Institute of Biomedical Imaging and Bioengineering | is listed by: SoftCite | NIH | Free, Available for download, Freely available | SCR_018365 | SEDFIT version 14.7g | 2026-02-11 10:59:45 | 25 | ||||||||
|
PRISMA Resource Report Resource Website 1000+ mentions |
PRISMA (RRID:SCR_018721) | PRISMA | portal, standard specification, data or information resource, narrative resource | Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions. | MDAR, standard, report standard, reporting reviews, randomized trial, evaluating randomized trial, reporting systematic review, intervention evaluation, meta analysis | is listed by: SoftCite | Ottawa Hospital Research Institute ; University of Oxford |
Free, Freely available | SCR_018721 | Preferred Reporting Items for Systematic Reviews and Meta-Analyses | 2026-02-11 10:59:47 | 1069 | |||||||
|
ELDA Resource Report Resource Website 100+ mentions |
ELDA (RRID:SCR_018933) | software application, production service resource, software resource, data analysis software, data processing software, service resource, analysis service resource | Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly. | Limiting dilution analysis, stem cell assay, data set confidence intervals, single hit hypothesis, adequacy test, frequency differences test | is listed by: SoftCite | PMID:19567251 | Free, Freely available | SCR_018933 | Extreme Limiting Dilution Analysis | 2026-02-11 10:59:49 | 385 | ||||||||
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PROCHECK Resource Report Resource Website 50+ mentions |
PROCHECK (RRID:SCR_019043) | software resource, software application, data processing software, data analysis software | Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR. | Stereochemical quality, protein structure, plot, residue listing, protein, assessing protein quality, | is listed by: SoftCite | DOI:10.1107/S0021889892009944 | Free, Available for download | SCR_019043 | 2026-02-11 10:59:55 | 75 | |||||||||
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CalcuSyn Resource Report Resource Website 50+ mentions |
CalcuSyn (RRID:SCR_020251) | software resource, software application, data processing software, data analysis software | Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools. | Biosoft, drug mixtures study, drug efficacy, dose effect, quantify synergism, quantify inhibition | is listed by: SoftCite | Restricted | SCR_020251 | CalcuSyn Version 2.0 | 2026-02-11 10:59:58 | 57 |
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