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:
CircSeqAlignTk_1.9.0.tar.gz
CircSeqAlignTk_1.9.0.zip(r-4.5)CircSeqAlignTk_1.9.0.zip(r-4.4)CircSeqAlignTk_1.9.0.zip(r-4.3)
CircSeqAlignTk_1.9.0.tgz(r-4.5-any)CircSeqAlignTk_1.9.0.tgz(r-4.4-any)CircSeqAlignTk_1.9.0.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-1.9.0(bioc 3.21)CircSeqAlignTk-1.8.0(bioc 3.20)
sequencingsmallrnaalignmentsoftware
Last updated 5 months agofrom:c5921ae086. Checks:2 OK, 4 NOTE, 3 ERROR. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 29 2025 |
| R-4.5-win | ERROR | Mar 29 2025 |
| R-4.5-mac | NOTE | Mar 29 2025 |
| R-4.5-linux | NOTE | Mar 29 2025 |
| R-4.4-win | ERROR | Mar 29 2025 |
| R-4.4-mac | NOTE | Mar 29 2025 |
| R-4.4-linux | NOTE | Mar 29 2025 |
| R-4.3-win | ERROR | Mar 29 2025 |
| R-4.3-mac | OK | Mar 29 2025 |
Exports:align_readsbuild_appbuild_indexcalc_coveragefilter_readsgenerate_readsget_slot_contentsplot_coverage
Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcachemclicodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdigestdplyrevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2hwriterigraphinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplotlypngprettyunitsprogresspromisespurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRbowtie2RColorBrewerRcppRcppEigenRCurlrestfulrRhisat2RhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerRUnitS4ArraysS4VectorssassscalesSGSeqshinyshinyFilesshinyjsShortReadsnowsourcetoolsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxml2xtableXVectoryaml
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 |