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Infrastructure shared by all the Biostrings-based genome data packages.

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This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources

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cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualizat

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Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various

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algorithm for determining cluster count and membership by stability evidence in unsupervised analysis

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A toolset for deciphering and managing biological sequences.

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Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working wit

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Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a

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