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This package provides an R wrapper for the popular Bowtie2 sequencing read aligner, optimized to run on NVIDIA graphics cards. It includes wrapper functions that enable both genome indexing and alignment to the generated indexes, ensuring high performance and ease of use within the R environment.
Rqc is an optimised tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.
Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.