This package is an automatically generated RnBeads annotation package for the assembly hg19.

This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.

This package provides a function to infer pathway activity from gene expression. It contains the linear model inferred in the publication "Perturbation-response genes reveal signaling footprints in cancer gene expression".

This package provides basic features for the automated analysis of Affymetrix arrays.

This package provides full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.

This package provides an implementation of an algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.

This package provides basic functions for filtering genes from high-throughput sequencing experiments.

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.

The two main functions in the package are pairwiseAlignment and stringDist. The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.

This package provides tools to support the analysis of RNA-seq expression data or other similar kind of data. It provides exploratory plots to evaluate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. It also supports the analysis of differential expression between two experimental conditions with no parametric assumptions.

Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15.

This package provides full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.

systemPipeRdata complements the systemPipeR workflow management system (WMS) by offering a collection of pre-designed data analysis workflow templates. These templates are easily accessible and can be readily loaded onto a user's system with a single command. Once loaded, the WMS can immediately utilize these templates for efficient end-to-end analysis, serving a wide range of data analysis needs.

GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. The gage package provides functions for basic GAGE analysis, result processing and presentation. In addition, it provides demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These functions and data are also useful for gene set analysis using other methods.

This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

This package provides methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package.

This package provides processed and raw count data for single-cell RNA sequencing. In addition, this package offers single-cell ATAC-seq, and seqFISH (spatial transcriptomic) experiments performed along a timecourse of mouse gastrulation and early organogenesis.

This package provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.

This package is a collection of Strand-seq data. The main purpose is to demonstrate functionalities of the breakpointR package.

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

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

This package provides a collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control.

This package provides raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type.