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 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.

Affymetrix Affymetrix RG_U34A Array annotation data (chip rgu34a) assembled using data from public repositories.

Generator of web pages which display interactive network/graph visualizations with D3js, jQuery and Raphael.

The ribor package provides an R Interface for .ribo files. It provides functionality to read the .ribo file, which is of HDF5 format, and performs common analyses on its contents.

Affymetrix ragene11 annotation data (chip ragene11sttranscriptcluster) assembled using data from public repositories.

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.

Vendors the igraph C source code and builds it into a static library. Other Bioconductor packages can link to libigraph.a in their own C/C++ code. This is intended for packages wrapping C/C++ libraries that depend on the igraph C library and cannot be easily adapted to use the igraph R package.

Functions, workflow, and a Shiny application for visualizing sequence conservation and designing degenerate primers, probes, and (RT)-(q/d)PCR assays from a multiple DNA sequence alignment. The results can be presented in data frame format and visualized as dashboard-like plots. For more information, please see the package vignette.

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 was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Rat230\_2\_probe\_tab.

Package that allows to explore the exposome and to perform association analyses between exposures and health outcomes.

This package provides a package containing an environment representing the RG_U34B.cdf file.

This package provides tools for comprehensive gene set enrichment and extraction of multi-resource high confidence subnetworks. RITAN facilitates bioinformatic tasks for enabling network biology research.

Affymetrix rta10 annotation data (chip rta10probeset) assembled using data from public repositories.

The RImmPort package simplifies access to ImmPort data for analysis in the R environment. It provides a standards-based interface to the ImmPort study data that is in a proprietary format.

Suite of tools for functional analysis.

This package provides a package for nonlinear dimension reduction using the Isomap and LLE algorithm. It also includes a routine for computing the Davis-Bouldin-Index for cluster validation, a plotting tool and a data generator for microarray gene expression data and for the Swiss Roll dataset.

Package provides clinical, expression, cnv and mutation data from Genome Cancer Browser.

RNA degradation is monitored through measurement of RNA abundance after inhibiting RNA synthesis. This package has functions and example scripts to facilitate (1) data normalization, (2) data modeling using constant decay rate or time-dependent decay rate models, (3) the evaluation of treatment or genotype effects, and (4) plotting of the data and models. Data Normalization: functions and scripts make easy the normalization to the initial (T0) RNA abundance, as well as a method to correct for artificial inflation of Reads per Million (RPM) abundance in global assessments as the total size of the RNA pool decreases. Modeling: Normalized data is then modeled using maximum likelihood to fit parameters. For making treatment or genotype comparisons (up to four), the modeling step models all possible treatment effects on each gene by repeating the modeling with constraints on the model parameters (i.e., the decay rate of treatments A and B are modeled once with them being equal and again allowing them to both vary independently). Model Selection: The AICc value is calculated for each model, and the model with the lowest AICc is chosen. Modeling results of selected models are then compiled into a single data frame. Graphical Plotting: functions are provided to easily visualize decay data model, or half-life distributions using ggplot2 package functions.

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

Provide functions to obtain instrumentation data on processes in a unix environment. Parse output of a collectl run. Vizualize aspects of system usage over time, with annotation.

Agilent annotation data (chip rgug4105a) assembled using data from public repositories.

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