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bioc
orthogene:Interspecies gene mapping
`orthogene` is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date gene ortholog mappings across **700+ organisms**. It also provides various utility functions to aggregate/expand common objects (e.g. data.frames, gene expression matrices, lists) using **1:1**, **many:1**, **1:many** or **many:many** gene mappings, both within- and between-species.
Maintained by Brian Schilder. Last updated 5 months ago.
geneticscomparativegenomicspreprocessingphylogeneticstranscriptomicsgeneexpressionanimal-modelsbioconductorbioconductor-packagebioinformaticsbiomedicinecomparative-genomicsevolutionary-biologygenesgenomicsontologiestranslational-research
43 stars 7.86 score 31 scripts 2 dependentsbioc
BridgeDbR:Code for using BridgeDb identifier mapping framework from within R
Use BridgeDb functions and load identifier mapping databases in R. It uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.
Maintained by Egon Willighagen. Last updated 5 months ago.
softwareannotationmetabolomicscheminformaticsbioconductor-packagebridgedbgenesidentifierslife-sciencesmetabolitesproteinsopenjdk
4 stars 6.97 score 43 scripts
zjwinn
HaploCatcher:A Predictive Haplotyping Package
Used for predicting a genotype’s allelic state at a specific locus/QTL/gene. This is accomplished by using both a genotype matrix and a separate file which has categorizations about loci/QTL/genes of interest for the individuals in the genotypic matrix. A training population can be created from a panel of individuals who have been previously screened for specific loci/QTL/genes, and this previous screening could be summarized into a category. Using the categorization of individuals which have been genotyped using a genome wide marker platform, a model can be trained to predict what category (haplotype) an individual belongs in based on their genetic sequence in the region associated with the locus/QTL/gene. These trained models can then be used to predict the haplotype of a locus/QTL/gene for individuals which have been genotyped with a genome wide platform yet not genotyped for the specific locus/QTL/gene. This package is based off work done by Winn et al 2021. For more specific information on this method, refer to <doi:10.1007/s00122-022-04178-w>.
Maintained by Zachary Winn. Last updated 11 months ago.
genesgeneticslocusmachine-learningmolecular-geneticspipelineplantbreeding
4.18 score 3 scriptsbioc
famat:Functional analysis of metabolic and transcriptomic data
Famat is made to collect data about lists of genes and metabolites provided by user, and to visualize it through a Shiny app. Information collected is: - Pathways containing some of the user's genes and metabolites (obtained using a pathway enrichment analysis). - Direct interactions between user's elements inside pathways. - Information about elements (their identifiers and descriptions). - Go terms enrichment analysis performed on user's genes. The Shiny app is composed of: - information about genes, metabolites, and direct interactions between them inside pathways. - an heatmap showing which elements from the list are in pathways (pathways are structured in hierarchies). - hierarchies of enriched go terms using Molecular Function and Biological Process.
Maintained by Mathieu Charles. Last updated 5 months ago.
functionalpredictiongenesetenrichmentpathwaysgoreactomekeggcompoundgene-ontologygenesshiny
1 stars 3.78 score 2 scripts