Use this package to create or update AnVIL workspaces from resources such as R / Bioconductor packages. The metadata about the package (e.g., select information from the package DESCRIPTION file and from vignette YAML headings) are used to populate the DASHBOARD'. Vignettes are translated to python notebooks ready for evaluation in AnVIL.

adverSCarial is an R Package designed for generating and analyzing the vulnerability of scRNA-seq classifiers to adversarial attacks. The package is versatile and provides a format for integrating any type of classifier. It offers functions for studying and generating two types of attacks, single gene attack and max change attack. The single-gene attack involves making a small modification to the input to alter the classification. The max-change attack involves making a large modification to the input without changing its classification. The CGD attack is based on an estimated gradient descent. against adversarial attacks. The package provides a comprehensive solution for evaluating the robustness of scRNA-seq classifiers against adversarial attacks.

This package contains pre-built human (GPL96) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO.

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The main cloud-based genomics platform deported by the AnVIL project is Terra. The AnVILWorkflow package allows remote access to Terra implemented workflows, enabling end-user to utilize Terra/ AnVIL provided resources - such as data, workflows, and flexible/scalble computing resources - through the conventional R functions.

The AWAggregatorData package contains the data associated with the AWAggregator R package. It includes two pre-trained random forest models, one incorporating the average coefficient of variation as a feature, and the other one not including it. It also contains the PSMs in Benchmark Set 1~3 derived from the psm.tsv output files generated by FragPipe, which are used to train the random forest models.

Data needed by the affycomp package.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was ATH1-121501\_probe\_tab.

Save SpatialExperiment objects and their images into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the frma package.

This package unifies access to Statistal Modeling of Omics Data. Across linear modeling engines (lm, lme, lmer, limma, and wilcoxon). Across coding systems (treatment, difference, deviation, etc). Across model formulae (with/without intercept, random effect, interaction or nesting). Across omics platforms (microarray, rnaseq, msproteomics, affinity proteomics, metabolomics). Across projection methods (pca, pls, sma, lda, spls, opls). Across clustering methods (hclust, pam, cmeans). Across survival methods (coxph, survdiff, coin). It provides a fast enrichment analysis implementation.

Assay for Transpose-Accessible Chromatin using sequencing (ATAC-seq) is a technique to assess genome-wide chromatin accessibility by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. ATACseqTFEA is an improvement of the current computational method that detects differential activity of transcription factors (TFs). ATACseqTFEA not only uses the difference of open region information, but also (or emphasizes) the difference of TFs footprints (cutting sites or insertion sites). ATACseqTFEA provides an easy, rigorous way to broadly assess TF activity changes between two conditions.

Supplies AnnotationHub with some preprocessed sqlite, tibble, and data.table datasets of PubMed. All the datasets are generated by our Snakemake workflow [pubmed-workflow](https://github.com/rikenbit/pubmed-workflow). For the details, see the README.md of pubmed-workflow.

Supplies AnnotationHub with `MeSHDb` NIH MeSH annotation databases for many species. All the SQLite files and metadata.csv are generated by our Snakemake workflow [mesh-workflow](https://github.com/rikenbit/mesh-workflow).

This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix Fusion SDK distribution and other official sources.

The package provides a comprehensive mapping table of metabolites and proteins linked to PathBank pathways. The tables include HMDB, KEGG, ChEBI, CAS, Drugbank, Uniprot IDs. The tables are provided for each of the 10 species ("Homo sapiens", "Escherichia coli", "Mus musculus", "Arabidopsis thaliana", "Saccharomyces cerevisiae", "Bos taurus", "Caenorhabditis elegans", "Rattus norvegicus", "Drosophila melanogaster", and "Pseudomonas aeruginosa"). These table information can be used for Metabolite Set (and other) Enrichment Analysis.

Supplies AnnotationHub with `LRbaseDb` Ligand-Receptor annotation databases for many species. All the SQLite files are generated by our Snakemake workflow [lrbase-workflow](https://github.com/rikenbit/lrbase-workflow). For the details, see the README.md of lrbase-workflow.

This package contains ARACNe-inferred networks from TCGA tumor datasets. It also contains a function to export them into plain-text format.

This package provides a package containing an environment representing the AG.CDF file.

Builds upon the existing ArtifactDB project, expending alabaster.spatial for language agnostic on disk serialization of SpatialFeatureExperiment.

The package provides a comprehensive mapping table of metabolites linked to Wikipathways pathways. The tables include HMDB, KEGG, ChEBI, Drugbank, PubChem compound, ChemSpider, KNApSAcK, and Wikidata IDs plus CAS and InChIKey. The tables are provided for each of the 25 species ("Anopheles gambiae", "Arabidopsis thaliana", "Bacillus subtilis", "Bos taurus", "Caenorhabditis elegans", "Canis familiaris", "Danio rerio", "Drosophila melanogaster", "Equus caballus", "Escherichia coli", "Gallus gallus", "Gibberella zeae", "Homo sapiens", "Hordeum vulgare", "Mus musculus", "Mycobacterium tuberculosis", "Oryza sativa", "Pan troglodytes", "Plasmodium falciparum", "Populus trichocarpa", "Rattus norvegicus", "Saccharomyces cerevisiae", "Solanum lycopersicum", "Sus scrofa", "Zea mays"). These table information can be used for Metabolite Set Enrichment Analysis.

ASSIGN is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literature or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature.

Data frame containing alternative splicing events. The splicing events were compiled from the annotation files used by the alternative splicing quantification tools MISO, VAST-TOOLS, SUPPA and rMATS.

Save variant calling SummarizedExperiment to file and load them back as VCF objects. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Annotation package for the implementation of the frozen Robust Multiarray Analysis procedure for Arabidopsis thaliana. This package was generated on the basis of frmaTools version 1.52.0.