Package: CircSeqAlignTk 1.15.0

Jianqiang Sun

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

CircSeqAlignTk is a toolkit for the analysis of RNA-Seq data derived from circular genome sequences, with a primary focus on viroids, circular RNAs typically consisting of a few hundred nucleotides. The toolkit supports an end-to-end analysis pipeline, from alignment to visualization.

Authors:Jianqiang Sun [cre, aut], Xi Fu [ctb], Wei Cao [ctb]

CircSeqAlignTk_1.15.0.tar.gz
CircSeqAlignTk_1.15.0.zip(r-4.7)CircSeqAlignTk_1.15.0.zip(r-4.6)CircSeqAlignTk_1.15.0.zip(r-4.5)
CircSeqAlignTk_1.15.0.tgz(r-4.6-any)CircSeqAlignTk_1.15.0.tgz(r-4.5-any)
CircSeqAlignTk_1.15.0.tar.gz(r-4.7-any)CircSeqAlignTk_1.15.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
card.svg |card.png
CircSeqAlignTk/json (API)
NEWS

# Install 'CircSeqAlignTk' in R:

install.packages('CircSeqAlignTk', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bitdessin/circseqaligntk/issues

On BioConductor:CircSeqAlignTk-1.15.0(bioc 3.24)CircSeqAlignTk-1.14.0(bioc 3.23)

sequencing smallrna alignment software

4.00 score 3 scripts 286 downloads 7 exports 147 dependencies

Last updated from:680cbf01d4. Checks:5 NOTE, 1 OK, 3 ERROR, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	231
linux-devel-x86_64	NOTE	548
source / vignettes	OK	414
linux-release-x86_64	NOTE	524
macos-release-arm64	NOTE	329
macos-oldrel-arm64	NOTE	216
windows-devel	ERROR	372
windows-release	ERROR	370
windows-oldrel	ERROR	414
wasm-release	FAIL	193

Exports:align_reads build_app build_index calc_coverage filter_reads generate_reads plot_coverage

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob bslib cachem cigarillo cli codetools commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir digest dplyr evaluate farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable highr hms htmltools htmlwidgets httpuv httr httr2 hwriter igraph interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime openssl otel pillar pkgconfig plotly png prettyunits progress promises purrr pwalign R.methodsS3 R.oo R.utils R6 rappdirs Rbowtie2 RColorBrewer Rcpp RcppEigen RCurl restfulr Rhisat2 Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer RUnit S4Arrays S4Vectors S7 sass scales Seqinfo SGSeq shiny shinyFiles shinyjs ShortRead snow sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 vctrs viridisLite withr xfun XML xml2 xtable XVector yaml

Documentation

Jianqiang Sun

Rendered fromCircSeqAlignTk.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-05-09
Started: 2022-08-09

Citation

Development and contributors

Readme and manuals

Help Manual

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