ontoProc - processing of ontologies of anatomy, cell lines, and so on
Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.
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infrastructuregobioinformaticsgenomicsontology
8.06 score 5 stars 2 dependents 91 scriptscombinat - combinatorics utilities
routines for combinatorics
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7.98 score 232 dependents 1000 scripts 34k downloadsROC - utilities for ROC, with microarray focus
Provide utilities for ROC, with microarray focus.
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differentialexpression
7.95 score 12 dependents 72 scripts 1.9k downloadsMLInterfaces - Uniform interfaces to R machine learning procedures for data in Bioconductor containers
This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.
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classificationclustering
7.73 score 5 dependents 80 scriptsgwascat - representing and modeling data in the EMBL-EBI GWAS catalog
Represent and model data in the EMBL-EBI GWAS catalog.
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genetics
6.66 score 2 dependents 155 scripts 1.6k downloadsBiocFHIR - Illustration of FHIR ingestion and transformation using R
FHIR R4 bundles in JSON format are derived from https://synthea.mitre.org/downloads. Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, https://www.kaggle.com/code/drscarlat/fhir-starter-parse-healthcare-bundles-into-tables. This is a very limited illustration of some basic parsing and reorganization processes. Additional tooling will be required to move beyond the Synthea data illustrations.
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infrastructuredataimportdatarepresentationfhir
6.00 score 4 stars 25 scripts 315 downloadsontoProc2 - Ontology Facilities Based on INCAtools Semantic SQL
This package provides ontology facilities based on INCAtools Semantic SQL. Tooling is provided to retrieve and cache SQLite databases representing curated ontologies. ontologyIndex ontology_index instances can be produced. Anthropic's Claude was used in the development of S7 classes and methods and in the production of documentation.
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infrastructuredatarepresentationpathwayssinglecell
5.01 score 1 dependents 19 scriptsparody - Parametric And Resistant Outlier DYtection
Provide routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics.
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multiplecomparison
4.82 score 1 dependents 22 scripts 548 downloadsPlinkMatrix - DelayedArray interface for plink bed files
This package provides a DelayedArray interface for plink bed files. There is support for interfacing to plink genotype data via RangedSummarizedExperiment. Example data from the GEUVADIS project (internationalgenome.org) are used for demonstration.
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infrastructuregeneticscpp
4.70 score 1 stars 10 scriptsBiocHail - basilisk and hail
Use hail via basilisk when appropriate, or via reticulate. This package can be used in terra.bio to interact with UK Biobank resources processed by hail.is.
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infrastructurebioconductorgeneticshail
4.58 score 6 stars 16 scriptsivygapSE - A SummarizedExperiment for Ivy-GAP data
Define a SummarizedExperiment and exploratory app for Ivy-GAP glioblastoma image, expression, and clinical data.
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transcriptionsoftwarevisualizationsurvivalgeneexpressionsequencing
4.43 score 18 scripts 418 downloadsAnVILBilling - Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org).
AnVILBilling helps monitor AnVIL-related costs in R, using queries to a BigQuery table to which costs are exported daily. Functions are defined to help categorize tasks and associated expenditures, and to visualize and explore expense profiles over time. This package will be expanded to help users estimate costs for specific task sets.
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infrastructuresoftware
4.30 score 5 scriptstenXplore - ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics
Perform ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics.
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immunooncologydimensionreductionprincipalcomponenttranscriptomicssinglecell
4.08 score 12 scripts 466 downloadsBiocSklearn - interface to python sklearn via Rstudio reticulate
This package provides interfaces to selected sklearn elements, and demonstrates fault tolerant use of python modules requiring extensive iteration.
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statisticalmethoddimensionreductioninfrastructure
4.08 score 12 scripts 420 downloadsRcollectl - Help use collectl with R in Linux, to measure resource consumption in R processes
Provide functions to obtain instrumentation data on processes in a unix environment. Parse output of a collectl run. Vizualize aspects of system usage over time, with annotation.
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softwareinfrastructure
4.07 score 3 stars 13 scripts 183 downloadsxenLite - Simple classes and methods for managing Xenium datasets
Define a relatively light class for managing Xenium data using Bioconductor. Address use of parquet for coordinates, SpatialExperiment for assay and sample data. Address serialization and use of cloud storage.
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infrastructureu24ca289073
4.00 score 1 stars 4 scriptspogos - PharmacOGenomics Ontology Support
Provide simple utilities for querying bhklab PharmacoDB, modeling API outputs, and integrating to cell and compound ontologies.
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pharmacogenomicspooledscreensimmunooncology
4.00 score 10 scriptsarrayMvout - multivariate outlier detection for expression array QA
This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate
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infrastructuremicroarrayqualitycontrol
3.82 score 11 scriptsaffyContam - structured corruption of affymetrix cel file data
structured corruption of cel file data to demonstrate QA effectiveness
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infrastructure
3.78 score 1 dependents 4 scriptsssrch - a simple search engine
Demonstrate tokenization and a search gadget for collections of CSV files.
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infrastructure
3.62 score 21 scriptsvtpnet - variant-transcription factor-phenotype networks
variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828
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network
3.30 score 6 scripts 462 downloadskeggorthology - graph support for KO, KEGG Orthology
graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs.
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pathwaysgraphandnetworkvisualizationkegg
3.30 score 8 scriptsRbcBook1 - Support for Springer monograph on Bioconductor
tools for building book
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software
3.30 score 2 scriptsTxParq.Hs.gencode.v49 - Parquet-based representation of GENCODE gene models v49 for Homo sapiens
This is a parquet-based representation of GENCODE gene models v49 for Homo sapiens. Parquet is chosen to reduce footprint, to support tidyverse-oriented operations natively, and to provide opportunities for cloud-backed annotation services. Community contributions to functionality and architecture are welcome.
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infrastructure
3.00 score 5 scriptsGO.ddb - Tidy Interface to GO Semantic SQL via DuckDB
Provides a tidyverse-oriented user interface to Gene Ontology data via the Semantic SQL representation, accessed through DuckDB. Replaces the GO.db + AnnotationDbi::select nexus with lazy tibble-based operations for term lookup, ancestor/descendant traversal, and gene-GO annotation queries. The Semantic SQL resource is managed by the ontoProc2 package via BiocFileCache.
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annotationgoontology
2.00 score 2 scripts