webchem - Chemical Information from the Web

Chemical information from around the web. This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.

Last updated 9 months ago

cas-numberchemical-informationchemspideridentifierropensciwebscraping

10.19 score 161 stars 9 packages 162 scripts 1.0k downloads

hoardr - Manage Cached Files

Suite of tools for managing cached files, targeting use in other R packages. Uses 'rappdirs' for cross-platform paths. Provides utilities to manage cache directories, including targeting files by path or by key; cached directories can be compressed and uncompressed easily to save disk space.

Last updated 10 months ago

cachingdatafilesxmlpdf

8.16 score 23 stars 39 packages 6 scripts 2.7k downloads

mulea - Enrichment Analysis using Multiple Ontologies and False Discovery Rate

Background - Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. Results - mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. mulea expands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardised GMT format) for 27 model organisms, covering 22 ontology types from 16 databases and various identifiers resulting in almost 900 files. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally, mulea's architecture allows for easy integration of user-defined ontologies, or GMT files from external sources (e.g., MSigDB or Enrichr), expanding its applicability across diverse research areas. Conclusions - mulea is distributed as a CRAN R package. It offers researchers a powerful and flexible toolkit for functional enrichment analysis, addressing limitations of traditional tools with its progressive eFDR and by supporting a variety of ontologies. Overall, mulea fosters the exploration of diverse biological questions across various model organisms.

Last updated 1 months ago

annotationdifferentialexpressiongeneexpressiongenesetenrichmentgographandnetworkmultiplecomparisonpathwaysreactomesoftwaretranscriptionvisualizationbioconductor-packageenrichmentenrichment-analysisfunctional-enrichment-analysisgene-set-enrichmentontologiestranscriptomics

7.32 score 21 stars 33 scripts 340 downloads

taxizedb - Tools for Working with 'Taxonomic' Databases

Tools for working with 'taxonomic' databases, including utilities for downloading databases, loading them into various 'SQL' databases, cleaning up files, and providing a 'SQL' connection that can be used to do 'SQL' queries directly or used in 'dplyr'.

Last updated 5 months ago

itistaxizetaxonomic-databasestaxonomy

6.36 score 30 stars 1 packages 84 scripts 73 downloads