This package provides a function that performs gene-permuting of a gene-set enrichment analysis (GSEA) calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.

This package provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.

This package lets you programmatically access the NIH/NCI Genomic Data Commons RESTful service.

The scRepertoire package was built to process data derived from the 10x Genomics Chromium Immune Profiling for both TCR and Ig enrichment workflows and subsequently interacts with the popular Seurat and SingleCellExperiment R packages. It also allows for general analysis of single-cell clonotype information without the use of expression information. The package functions as a wrapper for Startrac and powerTCR R packages.

This is a package for saving SummarizedExperiments into file artifacts, and loading 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.

This package is a visualization and analysis toolbox for short time course data which includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. The package also provides methods for retrieving enriched pathways.

This is a package to support identification of markers of rare cell types by looking at genes whose expression is confined in small regions of the expression space.

This package provides generic functions for interacting with the AnVIL system. Packages that use either GCP or Azure in AnVIL are built on top of AnVILBase. Extension packages will provide methods for interacting with other cloud providers.

This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

This package contains experimental genetic data for use with the genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.

This package provides an interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.

This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.

This package provides a client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various administrative and management tasks. Check out the documentation at https://github.com/ArtifactDB/gypsum-worker for more details.

This package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.

This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.

This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.

The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.

Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, RNA, coding sequence (CDS), GFF, and metagenome retrieval from NCBI RefSeq, NCBI Genbank, ENSEMBL, and UniProt databases. Furthermore, an interface to the BioMart database allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as NCBI RefSeq, NCBI nr, NCBI nt, NCBI Genbank, etc with only one command.

This package provides dataset samples (Affymetrix: Expression, Gene, Exon, SNP; NimbleGen: Expression, Tiling) to be used with the oligo package.

This package provides an implementation of an algorithm for determining cluster count and membership by stability evidence in unsupervised analysis.

This package contains gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata.

This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.

This package provides the lengths of mRNA transcripts for a number of genomes and gene ID formats, largely based on the UCSC table browser.

This package is used for the identification and validation of sequence motifs. It makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.