Package: CircSeqAlignTk 1.9.0

Jianqiang Sun

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

CircSeqAlignTk is designed for end-to-end RNA-Seq data analysis of circular genome sequences, from alignment to visualization. It mainly targets viroids which are composed of 246-401 nt circular RNAs. In addition, CircSeqAlignTk implements a tidy interface to generate synthetic sequencing data that mimic real RNA-Seq data, allowing developers to evaluate the performance of alignment tools and workflows.

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

CircSeqAlignTk_1.9.0.tar.gz

CircSeqAlignTk_1.9.0.tgz(r-4.4-any)CircSeqAlignTk_1.7.1.tgz(r-4.3-any)
CircSeqAlignTk_1.9.0.tar.gz(r-4.5-noble)CircSeqAlignTk_1.9.0.tar.gz(r-4.4-noble)
CircSeqAlignTk.pdf |CircSeqAlignTk.html✨
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/jsun/circseqaligntk/issues

On BioConductor:CircSeqAlignTk-1.7.1(bioc 3.20)CircSeqAlignTk-1.6.0(bioc 3.19)

sequencing smallrna alignment software

4.40 score 3 scripts 136 downloads 8 exports 150 dependencies

Last updated 22 days agofrom:c5921ae086. Checks:OK: 2 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-mac	NOTE	Oct 30 2024
R-4.3-mac	OK	Sep 21 2024

Exports:align_reads build_app build_index calc_coverage filter_reads generate_reads get_slot_contents plot_coverage

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob bslib cachem cli codetools colorspace commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir digest dplyr evaluate fansi farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData 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 mgcv mime munsell nlme openssl pillar pkgconfig plogr 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 sass scales 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 zlibbioc

CircSeqAlignTk: An R package for end-to-end analysis of RNA-seq data for circular genomes

Jianqiang Sun, Xi Fu, Wei Cao

Rendered fromCircSeqAlignTk.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-08-22
Started: 2022-08-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
CircSeqAlignTk: A toolkit for end-to-end analysis of RNA-seq data for circular genomes	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
Get the slot contents from a formal class	get_slot_contents
Merge multiple synthetic datasets	merge.CircSeqAlignTkSim
Visualize alignment coverage	plot.CircSeqAlignTkCoverage plot_coverage