End-to-End Analysis of Small RNA-Seq Data from Viroids


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Documentation for package ‘CircSeqAlignTk’ version 1.11.2

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CircSeqAlignTk-package CircSeqAlignTk: End-to-End Analysis of Small RNA-Seq Data from Viroids
align_reads Align sequence reads to a genome sequence
build_app Build a GUI application of CircSeqAlignTk
build_index Build indexes of reference sequences for alignment
calc_coverage Calculate alignment coverage
CircSeqAlignTk CircSeqAlignTk: End-to-End Analysis of Small RNA-Seq Data from Viroids
CircSeqAlignTkAlign-class Class to store alignment results
CircSeqAlignTkCoverage-class Class to save alignment coverage
CircSeqAlignTkRefIndex-class Class to store reference information
CircSeqAlignTkSim-class Class to save information of synthetic reads
filter_reads Filter sequence reads in a FASTQ file by length
generate_reads Generate synthetic sequence reads
merge.CircSeqAlignTkSim Merge multiple synthetic datasets
plot.CircSeqAlignTkCoverage Visualize alignment coverage
plot_coverage Visualize alignment coverage