RUVnormalize is meant to remove unwanted variation from gene expression data when the factor of interest is not defined, e.g., to clean up a dataset for general use or to do any kind of unsupervised analysis.

This package provides a collection of methods for performing random rotations on high-dimensional, normally distributed data (e.g. microarray or RNA-seq data) with batch structure. The random rotation approach allows exact testing of dependent test statistics with linear models following arbitrary batch effect correction methods.

Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) running locally to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.

This package was created with the help of frmaTools version 1.24.0.

This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.

Affymetrix raex10 annotation data (chip raex10sttranscriptcluster) assembled using data from public repositories.

RNAeditr analyzes site-specific RNA editing events, as well as hyper-editing regions. The editing frequencies can be tested against binary, continuous or survival outcomes. Multiple covariate variables as well as interaction effects can also be incorporated in the statistical models.

Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape.

Generate HTML or PDF reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder. You can also create reports for DESeq2 or edgeR results.

This package implements the QUBIC algorithm introduced by Li et al. for the qualitative biclustering with gene expression data.

This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.

Improves simultaneous inference under dependence of tests by estimating a collapsed null distribution through resampling. Accounting for the dependence between tests increases the power while reducing the variability of the false discovery proportion. This dependence is common in genomics applications, e.g. when combining flow cytometry measurements with microbiome sequence counts.

Clontech BD Atlas Long Oligos Rat 4K annotation data (chip rguatlas4k) assembled using data from public repositories.

Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.

rfaRm provides a client interface to the Rfam database of RNA families. Data that can be retrieved include RNA families, secondary structure images, covariance models, sequences within each family, alignments leading to the identification of a family and secondary structures in the dot-bracket format.

R package for performing thermal proximity co-aggregation analysis with thermal proteome profiling datasets to analyse protein complex assembly and (differential) protein-protein interactions across conditions.

This package provides a package containing an environment representing the RaGene-1_0-st-v1.cdf file.

Affymetrix Affymetrix RAE230B Array annotation data (chip rae230b) assembled using data from public repositories.

Data such as is contained in the two R data files in this package are required for the RITAN package examples. Users are highly encouraged to use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes and RITAN.md for more information, such as gathering more up-to-date annotation data.

Affymetrix Affymetrix RT_U34 Array annotation data (chip rtu34) assembled using data from public repositories.

This package analyze spatial transcriptomics data through cross-regional cell type-specific analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.

Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot.

This package provides a web interface to compute transcriptional regulatory modules with rTRM.

Affymetrix ragene20 annotation data (chip ragene20stprobeset) assembled using data from public repositories.