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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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r8s Resource Report Resource Website 10+ mentions |
r8s (RRID:SCR_021161) | software toolkit, software resource | Software package for estimating absolute rates of molecular evolution and divergence times on phylogenetic tree. Divergence time estimation on phylogenies. | Divergence time estimation, phylogenies, estimating absolute rates, molecular evolution, divergence times, phylogenetic tree | Free, Available for download, Freely available | SCR_021161 | 2026-08-09 09:07:30 | 14 | |||||||||||
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BME Resource Report Resource Website 1+ mentions |
BME (RRID:SCR_021953) | software toolkit, software resource | Software Python package to construct conformational ensemble of biomolecular system by integrating molecular simulations and experimental data. Performs ensemble reweighting using Bayesian Maximum Entropy approach. | Bayesian maximum entropy, integrating molecular simulations and experimental data, ensemble reweighting, Bayesian Maximum Entropy approach | The Velux Foundations ; Novo Nordisk Foundation ; Lundbeck Foundation |
PMID:32006288 | Free, Available for download, Freely available | SCR_021953 | Bayesian/Maximum Entropy | 2026-08-09 09:07:45 | 4 | ||||||||
|
Artistoo Resource Report Resource Website 1+ mentions |
Artistoo (RRID:SCR_020983) | software toolkit, software resource | Software toolbox, formerly called CPMjs, as framework to build interactive, explorable simulation models of cells and tissues in web browser. JavaScript library to build interactive Cellular Potts Models as command line applications or in web browser. | Cellular Potts Models, simulation models building, cells simulation models, tissue simulation models, JavaScript library, build interactive models | DOI:10.1101/2020.05.01.072975 | Free, Freely available | biotools:artistoo | https://github.com/ingewortel/artistoo, https://bio.tools/artistoo | SCR_020983 | Artificial Tissue Toolbox | 2026-08-09 09:07:54 | 2 | |||||||
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MLSBM Resource Report Resource Website 1+ mentions |
MLSBM (RRID:SCR_021795) | software toolkit, software resource | Software R package to Fit Bayesian stochastic block models and multi level stochastic block models using efficient Gibbs sampling implemented in Rcpp. Models assume symmetric, non reflexive graphs with unweighted, binary edges. Data are input as symmetric binary adjacency matrix, or list of such matrices. | Fit Bayesian stochastic block models, multi level stochastic block models, Gibbs sampling, Rcpp | Free, Available for download, Freely available | SCR_021795 | Efficient Estimation of Bayesian SBMs and MLSBMs | 2026-08-09 09:08:16 | 2 | ||||||||||
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gtsummary Resource Report Resource Website 10+ mentions |
gtsummary (RRID:SCR_021319) | software toolkit, software resource | Software R package creating customizable presentation ready tables, summarizing data sets, regression models, and more. Used for publication ready data summary and analytic result tables. | Publication ready data summary, customizable presentation ready tables, summarizing data sets, regression models, creating presentation ready data tables, data tables, data summary | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/ddsjoberg/gtsummary | SCR_021319 | 2026-08-09 09:07:32 | 15 | |||||||||
|
bam-lorenz-coverage Resource Report Resource Website 1+ mentions |
bam-lorenz-coverage (RRID:SCR_021837) | software toolkit, software resource | Software package to generate Lorenz plots and Coverage plots, directly from BAM file. It can also output tables as text documents so you can generate custom plots. There is also support to only analyse specific regions. | Lorenz plots generation, coverage plots generatio, plot generation directly from BAM files | Free, Available for download, Freely available | SCR_021837 | 2026-08-09 09:08:05 | 1 | |||||||||||
|
Catboost Resource Report Resource Website 50+ mentions |
Catboost (RRID:SCR_021694) | software toolkit, software resource | Software package for gradient boosting on decision trees library. Used for ranking, classification, regression and other ML tasks. | Gradient boosting, decision trees | Free, Available for download, Freely available | SCR_021694 | 2026-08-09 09:08:03 | 66 | |||||||||||
|
PretextView Resource Report Resource Website 100+ mentions |
PretextView (RRID:SCR_022024) | software application, software resource | Software tool to enable visualization from PretextMap output. Desktop application for viewing pretext contact maps. OpenGL Powered Pretext Contact Map Viewer. | visualization from PretextMap output, viewing pretext contact maps, map viewer | works with: PretextMap | Free, Available for download, Freely available | SCR_022024 | Wellcome Sanger Institute's High-Performance Assembly Group's Paired REad TEXTure Viewer, REad TEXTure Viewer | 2026-08-09 09:08:09 | 448 | |||||||||
|
PRISMA2020 Resource Report Resource Website 10+ mentions |
PRISMA2020 (RRID:SCR_021053) | software toolkit, software resource | Software R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams. ShinyApp for producing PRISMA 2020 compliant flow diagrams. | PRISMA 2020 compliant flow diagrams, producing flow diagrams, ShinyApp | Free, Available for download, Freely available | https://github.com/nealhaddaway/PRISMA2020/tree/0.0.1, https://zenodo.org/record/4287835#.YGyXuuhKhPZ | SCR_021053 | 2026-08-09 09:07:56 | 49 | ||||||||||
|
LEA Resource Report Resource Website 1+ mentions |
LEA (RRID:SCR_022020) | software toolkit, software resource | Software R package for landscape and ecological associations studies.Dedicated to genomewide association tests in general, with emphasis on association with ecological gradients. Runs analyses of population structure and scans for genomic signatures of local adaptation. | genomewide association tests, estimating ancestry coefficients, large genotypic matrices, evaluating number of ancestral populations, performing population differentiation tests of neutrality, identifying genetic polymorphisms | is related to: R Project for Statistical Computing | DOI:10.1111/2041-210X.12382 | Free, Available for download, Freely available | https://github.com/bcm-uga/LEA, https://bioconductor.org/packages/LEA/ | SCR_022020 | Landscape and Ecological Associations | 2026-08-09 09:07:47 | 3 | |||||||
|
pb assembly Resource Report Resource Website 10+ mentions |
pb assembly (RRID:SCR_021967) | software toolkit, software resource | Software tool as PacBio assembly tool suite. | Reads in, assembly out, PacBio assembly | Free, Available for download, Freely available | SCR_021967 | pb-assembly | 2026-08-09 09:08:18 | 13 | ||||||||||
|
plyranges Resource Report Resource Website 1+ mentions |
plyranges (RRID:SCR_021324) | software toolkit, software resource | Open source software R package for interacting with common Bioconductor classes Ranges and GenomicRanges. Grammar of genomic data transformation. Provides grammatical and consistent way of manipulating these classes to increase accessiblity for new Bioconductor users. | genomic data transformation, genomic data transformation grammar, genomic data, data transformation, | DOI:10.1186/s13059-018-1597-8 | Free, Available for download, Freely available | https://github.com/sa-lee/plyranges | SCR_021324 | 2026-08-09 09:08:02 | 1 | |||||||||
|
ChIPseeker Resource Report Resource Website 100+ mentions |
ChIPseeker (RRID:SCR_021322) | software toolkit, software resource | Software package to retrieve nearest genes around peak, annotate genomic region of peak, implements statstical methods for estimate significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare own dataset with those deposited in database.Several visualization functions are implemented to summarize coverage of peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes. | Retrieve nearest genes around peak, annotate genomic region of peak, overlap estimate significance, ChIP peak data sets |
uses: Gene Expression Omnibus (GEO) is listed by: Bioconductor |
PMID:25765347 | Free, Available for download, Freely available | SCR_021322 | 2026-08-09 09:07:32 | 364 | |||||||||
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GBRS Resource Report Resource Website 1+ mentions |
GBRS (RRID:SCR_020963) | software toolkit, software resource | Software suite of tools for reconstructing genomes using RNA-Seq data from multiparent population and for quantifying allele specific expression. | Reconstructing genomes, RNA-Seq data, multiparent population, quantifying allele specific expression | has parent organization: Jackson Laboratory | Free, Available for download, Freely available | SCR_020963 | 2026-08-09 09:07:54 | 5 | ||||||||||
|
survival Resource Report Resource Website 500+ mentions |
survival (RRID:SCR_021137) | software toolkit, software resource | Software R package contains core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models. | Survival analysis routines, Surv objects, Kaplan-Meier curve, Aalen-Johansen curve, Cox models, parametric accelerated failure time models |
is listed by: CRAN is listed by: SoftCite |
Free, Available to download, Freely available | https://github.com/therneau/survival | SCR_021137 | 2026-08-09 09:07:29 | 566 | |||||||||
|
pysam Resource Report Resource Website 100+ mentions |
pysam (RRID:SCR_021017) | software toolkit, software resource | Software tool as interface for reading and writing SAM files. Python module to read and manipulate mapped short read sequence data stored in SAM/BAM files. Lightweight wrapper of htslib C-API. | Interface, reading SAM files, writing SAM files, mapped short read sequence data, htslib C-API wrapper, SAM/BAM files |
is related to: SAMTOOLS is related to: SAM |
Free, Available for download, Freely available | https://github.com/pysam-developers/pysam | SCR_021017 | 2026-08-09 09:07:28 | 164 | |||||||||
|
caret Resource Report Resource Website 50+ mentions |
caret (RRID:SCR_021138) | software toolkit, software resource | Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality. | Plotting classification, regression models, data splitting, pre processing, feature selection, model tuning using resampling, estimation |
is listed by: CRAN is listed by: SoftCite |
Free, Available for download, Freely available | https://github.com/topepo/caret/ | SCR_021138 | Classification And REgression Training | 2026-08-09 09:07:54 | 96 | ||||||||
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BonVision Resource Report Resource Website 1+ mentions |
BonVision (RRID:SCR_021534) | software toolkit, software resource | Open source software package for creating and controlling visual environments.Software package for Bonsai which allows for control of 2D and 3D environments. | Creating visual environments, controlling visual environments, Bonsai, 2D environment, 3D environments, OpenBehavior |
is listed by: OpenBehavior is related to: BonVision project |
DOI:10.1101/2020.03.09.983775 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/bonvision/ | SCR_021534 | 2026-08-09 09:08:09 | 1 | ||||||||
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Tracker MRI Resource Report Resource Website 1+ mentions |
Tracker MRI (RRID:SCR_021816) | software toolkit, software resource | Software package for experimental control from Vision and Cognition Lab at Netherlands Institute for Neuroscience. Matlab based software for fMRI, Psychophysical experimentation and NHP training, with eye control using Measurement and Computing IO card. Interfaces with ISCAN eye tracker and communicates with the MRI console using trigger pulses. Uses Psychtoolbox3 graphics and control engine. | vision and cognition, experimental control, fMRI, psychophysical experimentation, NHP training, eye control, eye tracker | has parent organization: Royal Netherlands Academy of Arts and Sciences; Amsterdam; Netherlands | Free, Available for download, Freely available | SCR_021816 | Tracker-MRI | 2026-08-09 09:08:17 | 1 | |||||||||
|
ISA API Resource Report Resource Website 1+ mentions |
ISA API (RRID:SCR_020980) | software toolkit, software resource | Open platform for interoperable life science experimental metadata. Metadata framework as set of community specifications and software tools for enabling discovery, exchange and publication of metadata from experiments in life sciences. Python library for creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats.Provides programmatic metadata handling functionality to support automation, common interface and interoperable medium between two ISA formats, as well as with other life science data formats required for depositing data in public databases. | Interoperable life science platform, experimental metadata platform, ISA-Tab format, ISA-JSON format, depositing data formats, public databases depositing data format | DOI:10.1101/2020.11.13.382119 | Free, Available for download, Freely available | SCR_020980 | Investigation Study Assay API | 2026-08-09 09:07:54 | 1 |
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