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Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

Extends string parsing capabilities for genomic coordinates, supporting various formats including comma-separated numbers, space-delimited coordinates, and automatic detection of GRanges, GPos, and GInteractions objects.

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

Functions to add metadata to ExperimentHub db and resource files to AWS S3 buckets.

This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.

Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames.

CIGAR stands for Concise Idiosyncratic Gapped Alignment Report. CIGAR strings are found in the BAM files produced by most aligners and in the AIRR-formatted output produced by IgBLAST. The cigarillo package provides functions to parse and inspect CIGAR strings, trim them, turn them into ranges of positions relative to the "query space" or "reference space", and project positions or sequences from one space to the other. Note that these operations are low-level operations that the user rarely needs to perform directly. More typically, they are performed behind the scene by higher-level functionality implemented in other packages like Bioconductor packages GenomicAlignments and igblastr.

chimeraviz manages data from fusion gene finders and provides useful visualization tools.

A set of tools to forge BSgenome data packages. Supersedes the old seed-based tools from the BSgenome software package. This package allows the user to create a BSgenome data package in one function call, simplifying the old seed-based process.

The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.

Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and 'experiment data' packages.

This package provides repository information for the appropriate version of Bioconductor.

This package allows interactive viewing of package maintainer information. The Bioconductor Package Maintainer Application sends yearly verification emails to accept Bioconductor policies; this application also depicts maintainer status on opting in and if the email is deemed valid.

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.

The package defines many S4 generic functions used in Bioconductor.

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.

BiocCheck guides maintainers through Bioconductor best practicies. It runs Bioconductor-specific package checks by searching through package code, examples, and vignettes. Maintainers are required to address all errors, warnings, and most notes produced.

Functions that are needed by many other packages or which replace R functions.

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

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.

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.

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.

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides programatic access to the Dockstore, Leonardo, Rawls, TDR, and Terra RESTful programming interfaces. For platform-specific user-level functionality, see either the AnVILGCP or AnVILAz package.

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

structured corruption of cel file data to demonstrate QA effectiveness