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 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.

This is an R package to make it easier to import and store phylogenetic trees with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic trees with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.

This package provides an array-like container for convenient access and manipulation of HDF5 datasets. It supports delayed operations and block processing.

This package supports data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.

The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.

The fishpond package contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains a number of utilities for working with Salmon and Alevin quantification files.

The package AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to:

• analyze germline epimutations in the context of multi-generational mutation accumulation lines;

• analyze somatic epimutations in the context of plant development and aging.

This package provides a package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.

This package is an R program for the subset-based analysis of heterogeneous traits and disease subtypes. ASSET allows the user to search through all possible subsets of z-scores to identify the subset of traits giving the best meta-analyzed z-score. Further, it returns a p-value adjusting for the multiple-testing involved in the search. It also allows for searching for the best combination of disease subtypes associated with each variant.

This package provides a new clustering algorithm, binary cut, for clustering similarity matrices of functional terms is implemented in this package. It also provides functionalities for visualizing, summarizing and comparing the clusterings.

The parody package provides routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics.

In this package, a Hidden Semi Markov Model (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.

It has been shown that both DNA methylation and RNA transcription are linked to chronological age and age related diseases. Several estimators have been developed to predict human aging from DNA level and RNA level. Most of the human transcriptional age predictor are based on microarray data and limited to only a few tissues. To date, transcriptional studies on aging using RNASeq data from different human tissues is limited. The aim of this package is to provide a tool for across-tissue and tissue-specific transcriptional age calculation based on GTEx RNASeq data.

This package is an R package that offers models and tools for subject level analysis of X chromosome inactivation (XCI) and XCI-escape inference.

This package provides a Poisson mixture model is implemented to cluster genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).

This package provides functions for handling data from Bioconductor Affymetrix annotation data packages. It produces compact HTML and text reports including experimental data and URL links to many online databases. It allows searching of biological metadata using various criteria.

The package provides a set of functions to interact with the Google Cloud Platform (GCP) services on the AnVIL platform. The package is designed to work with the AnVIL package. User-level interaction with this package should be minimal.

This package provides support for numerical and graphical summaries of RNA-Seq genomic read data. Provided within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization. Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization.

This package provides an implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.

This is a comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. It provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.

This package provides a manifest package for Illumina's EPIC v2.0 methylation arrays. The version 2 covers more than 935K CpG sites in the human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K methylation array).

This package provides SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be injected in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).

MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for:

• covariate-controlled batch- and cohort effect adjustment;

• meta-analysis differential abundance testing;

• meta-analysis unsupervised discrete structure (clustering) discovery;

• meta-analysis unsupervised continuous structure discovery.