rtracklayer

Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNA-seq (short/long) by tools such as Kallisto, Salmon, StringTie, Tallon, IsoQuant etc.

'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques, geneXtendeR considers peak annotations beyond just the closest gene, allowing users to see peak summary statistics for the first-closest gene, second-closest gene, ..., n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene's coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.

CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.

Low- and high-level wrappers for Gemma's RESTful API. They enable access to curated expression and differential expression data from over 10,000 published studies. Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles.

The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.