Introduction | Installation | Preparation of working directory | Quick start | Implementation | Two-stage alignment process | Generation of reference sequences | Alignment | Summarization and visualization of alignment results | Synthetic small RNA-Seq data | Generation of synthetic sequence reads | Examples of sequence read generation with additional paramaters | Performance evaluation with the synthetic data | Case studies | A simulation study to evaluate the performance of the workflow | Analysis of small RNA-Seq data from vioid-infected tomato plants | GUI mode of CircSeqAlignTk | Session Information | References
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:
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✨
DESCRIPTION |NEWS
card.svg |card.png
CircSeqAlignTk/json (API)
| # 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)
sequencingsmallrnaalignmentsoftware
Last updated from:680cbf01d4. Checks:1 WARNING, 4 NOTE, 1 OK, 3 ERROR, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 241 | ||
| linux-devel-x86_64 | NOTE | 523 | ||
| source / vignettes | OK | 413 | ||
| linux-release-x86_64 | NOTE | 516 | ||
| macos-release-arm64 | NOTE | 298 | ||
| macos-oldrel-arm64 | NOTE | 284 | ||
| windows-devel | ERROR | 412 | ||
| windows-release | ERROR | 416 | ||
| windows-oldrel | ERROR | 338 | ||
| wasm-release | FAIL | 200 |
Exports:align_readsbuild_appbuild_indexcalc_coveragefilter_readsgenerate_readsplot_coverage
Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcachemcigarilloclicodetoolscommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdigestdplyrevaluatefarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2hwriterigraphinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpillarpkgconfigplotlypngprettyunitsprogresspromisespurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRbowtie2RColorBrewerRcppRcppEigenRCurlrestfulrRhisat2RhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerRUnitS4ArraysS4VectorsS7sassscalesSeqinfoSGSeqshinyshinyFilesshinyjsShortReadsnowsourcetoolsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxml2xtableXVectoryaml
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 |
