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

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Documentation for package ‘CircSeqAlignTk’ version 1.11.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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