This package provides processed 22 samples from BrainSpan keeping only the information for chromosome 21. Data is stored in the BigWig format and is used for examples in other packages.

EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of whole blood, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies.

Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

This is a package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface).

This is a package to perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.

BAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with rstan. It provides as output the stanfit object as well as posterior median and credible interval estimates for each correlation element.

This package implements two functions. One of them reads an Affymetrix CDF and creates a hash table environment containing the location/probe set membership mapping. The other one creates a package that automatically loads that environment.

TrackViewer offers multi-omics analysis with web based tracks and lollipops. Visualize mapped reads along with annotation as track layers for NGS datasets such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.

The package detects extended diffuse and compact blemishes on microarray chips. Harshlight marks the areas in a collection of chips (affybatch objects). A corrected AffyBatch object will result. The package replaces the defected areas with N/As or the median of the values of the same probe. The new version handles the substitute value as a whole matrix to solve the memory problem.

This package provides the output of running various transcript abundance quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The quantifiers were Cufflinks, RSEM, kallisto, Salmon and Sailfish. Alevin example output is also included.

This package provides infrastructure for parallel computations distributed by file or by range. User defined mapper and reducer functions provide added flexibility for data combination and manipulation.

This package provides the data that were used in the http://quinlanlab.org/tutorials/bedtools/bedtools.html. It includes a subset of the DnaseI hypersensitivity data from "Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were originally downloaded from the UCSC table browser. See the HelloRanges vignette for a port of the bedtools tutorial to R.

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model fruit fly Drosophila melanogaster.

Human Phenotype Ontology (HPO) was developed to create a consistent description of gene products with disease perspectives, and is essential for supporting functional genomics in disease context. Accurate disease descriptions can discover new relationships between genes and disease, and new functions for previous uncharacteried genes and alleles.

This package speeds up the derfinder package when using multiple cores. It is particularly useful when using BiocParallel and it helps reduce the time spent loading the full derfinder package when running the F-statistics calculation in parallel.

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 classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

This is a package to perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113).

This package ADAMgui is a graphical user interface (GUI) for the ADAM package. The ADAMgui package provides two shiny-based applications that allows the user to study the output of the ADAM package files through different plots. It's possible, for example, to choose a specific group of functionally associated genes (GFAG) and observe the gene expression behavior with the plots created with the GFAGtargetUi function. Features such as differential expression and fold change can be easily seen with aid of the plots made with the GFAGpathUi function.

Gcrma adjusts for background intensities in Affymetrix array data which include optical noise and non-specific binding (NSB). The main function gcrma converts background adjusted probe intensities to expression measures using the same normalization and summarization methods as a Robust Multiarray Average (RMA). Gcrma uses probe sequence information to estimate probe affinity to NSB. The sequence information is summarized in a more complex way than the simple GC content. Instead, the base types (A, T, G or C) at each position along the probe determine the affinity of each probe. The parameters of the position-specific base contributions to the probe affinity is estimated in an NSB experiment in which only NSB but no gene-specific binding is expected.

MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.

This package can do differential expression analysis of RNA-seq expression profiles with biological replication. It implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. It be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.

This package provides tools to calculate functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships, and so on.

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