# A toolkit for end-to-end analysis of RNA-seq data for circular genomes

## Documentation for package ‘CircSeqAlignTk’ version 1.0.0

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

## Help Pages

CircSeqAlignTk-package | CircSeqAlignTk: A toolkit for end-to-end analysis of RNA-seq data for circular genomes
align_reads | Align sequence reads to a genome sequence
build_index | Build indexes of reference sequences for alignment
calc_coverage | Calculate alignment coverage
CircSeqAlignTk | CircSeqAlignTk: A toolkit for end-to-end analysis of RNA-seq data for circular genomes
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
get_slot_contents | Get the slot contents from a formal class
merge.CircSeqAlignTkSim | Merge multiple synthetic datasets
plot.CircSeqAlignTkCoverage | Visualize alignment coverage
plot_coverage | Visualize alignment coverage