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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Worm Behavior Platform Resource Report Resource Website |
Worm Behavior Platform (RRID:SCR_021501) | software toolkit, software resource | Software tool as repository of documentation, software, and discussions to share worm tracking data and analysis routines.Open access repository for storing, accessing, and filtering data; interchange format for notating single or multi worm behavior; and file formats written in Python for feature extraction, review, and analysis. | Worm behavior data analysis, worm behavior data sharing, worm behavior data, Caenorhabditis elegans behavioral data, Worm tracker Commons Object Notation, OpenBehavior |
is listed by: OpenBehavior is related to: Worm Behavior Platform project |
DOI:10.1038/s41592-018-0112-1 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/worm-behavior-platform/ | SCR_021501 | Tracker Commons | 2026-08-09 09:08:08 | 0 | |||||||
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Data independent acquisition proteomics workbench Resource Report Resource Website 100+ mentions |
Data independent acquisition proteomics workbench (RRID:SCR_021862) | software toolkit, software resource | Software tools for analysis of data independent acqusition type proteomics data are implemented in Galaxy framework. Enables complete DIA data analysis including spectral library generation based on DDA type data, analysis of DIA data in raw or mzml format, and differntial statistical analysis. All tools are based on open-source software such as diypasef, OpenSwath, swath2stats and MSstats. | data independent acqusition, proteomics data, Galaxy framework, | has parent organization: University of Freiburg; Baden-Wurttemberg; Germany | DOI:10.1101/2021.07.21.453197 | Free, Freely available | SCR_021862 | 2026-08-09 09:07:44 | 441 | |||||||||
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Motif Alteration Genome wide to Globally Investigate Elements Resource Report Resource Website 1+ mentions |
Motif Alteration Genome wide to Globally Investigate Elements (RRID:SCR_021903) | MAGGIE | software toolkit, software resource | Software Python package for identifying motifs mediating transcription factor binding and function. Links mutations of motif to changes of epigenomic feature without assuming linear relationship. | Identifying motifs mediating transcription factor binding, identifying motifs mediating transcription factor function, motif mutations, epigenomic feature changes | NIDDK R01 DK091183; Foundation Leducq ; Netherlands Organization for Scientific Research ; Amsterdam Cardiovascular Sciences |
PMID:32657363 | Free, Available for download, Freely available | SCR_021903 | 2026-08-09 09:07:44 | 3 | ||||||||
|
scRNAx Resource Report Resource Website |
scRNAx (RRID:SCR_022091) | software toolkit, software resource | Software pipeline to improve gene annotation for cross species analysis of single cell RNA-Seq. Cross-species transfer of high quality 3’UTR annotation for single cell RNA-Seq. | scRNA-Seq cross-species gene annotation, cross species analysis, single cell RNA-Seq | Free, Available for download, Freely available | SCR_022091 | 2026-08-09 09:08:19 | 0 | |||||||||||
|
ProtHint Resource Report Resource Website 50+ mentions |
ProtHint (RRID:SCR_021167) | software toolkit, software resource | Software pipeline for predicting and scoring hints (in form of introns, start and stop codons) in genome of interest by mapping and spliced aligning predicted genes to database of reference protein sequences. | Predicting and scoring hints, form of introns, start and stop codons, genome, mapping, spliced aligning, predicted genes, database, reference protein sequences | has parent organization: Georgia Institute of Technology; Georgia; USA | Free, Available for download, Freely available | SCR_021167 | 2026-08-09 09:07:30 | 51 | ||||||||||
|
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 | |||||||||||
|
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 | |||||||
|
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 | ||||||||||
|
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 | |||||||||
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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 | ||||||||||
|
pcadapt Resource Report Resource Website 1+ mentions Issue |
pcadapt (RRID:SCR_022019) | software toolkit, software resource | 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 | 2026-08-09 09:08:19 | 3 | ||||||||
|
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 |
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