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

## Documentation for package ‘CircSeqAlignTk’ version 1.15.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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