1 Introduction | 1.1 Instalation and loading | 2 Data manipulation and overall usage | 2.1 GUI | 2.2 Command Line | 2.2.1 List of functions and their description | runPsScan() | readPsa() and readProsite() | gff2matrix() | matrix2hm() and matrixToSquareHeatmap() | extractSegments() and extractProteinMotifs() | extractProteinMotifs() | freqPie() | References | Session Information
Package: PMScanR 1.3.0
Jan Pawel Jastrzebski
PMScanR: Protein motifs analysis and visualisation
Provides tools for large-scale protein motif analysis and visualization in R. PMScanR facilitates the identification of motifs using external tools like PROSITE's ps_scan (handling necessary file downloads and execution) and enables downstream analysis of results. Key features include parsing scan outputs, converting formats (e.g., to GFF-like structures), generating motif occurrence matrices, and creating informative visualizations such as heatmaps, sequence logos (via seqLogo/ggseqlogo). The package also offers an optional Shiny-based graphical user interface for interactive analysis, aiming to streamline the process of exploring motif patterns across multiple protein sequences.
Authors:
PMScanR_1.3.0.tar.gz
PMScanR_1.3.0.zip(r-4.7)PMScanR_1.3.0.zip(r-4.6)PMScanR_1.3.0.zip(r-4.5)
PMScanR_1.3.0.tgz(r-4.6-any)PMScanR_1.3.0.tgz(r-4.5-any)
PMScanR_1.3.0.tar.gz(r-4.7-any)PMScanR_1.3.0.tar.gz(r-4.6-any)
PMScanR_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PMScanR/json (API)
| # Install 'PMScanR' in R: |
| install.packages('PMScanR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/prodakt/pmscanr/issues
On BioConductor:PMScanR-1.3.0(bioc 3.24)PMScanR-1.2.0(bioc 3.23)
Last updated from:c144ba8543. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 227 | ||
| linux-devel-x86_64 | OK | 447 | ||
| source / vignettes | OK | 322 | ||
| linux-release-x86_64 | OK | 392 | ||
| macos-release-arm64 | OK | 216 | ||
| macos-oldrel-arm64 | OK | 193 | ||
| windows-devel | OK | 325 | ||
| windows-release | OK | 296 | ||
| windows-oldrel | OK | 267 | ||
| wasm-release | OK | 247 |
Exports:extractProteinMotifsextractSegmentsfreqPiegff2matrixmatrix2hmmatrixToSquareHeatmapreadPrositereadPsarunPMScanRShinyrunPsScan
Dependencies:abindade4askpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbslibcachemcigarilloclicodetoolscommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdplyrevaluatefarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2ggseqlogogluegtablehighrhtmltoolshtmlwidgetshttpuvhttrhttr2IRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslotelpillarpixmappkgconfigplotlyplyrpromisespurrrR6rappdirsRColorBrewerRcppRcppArmadilloRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalessegmentedSeqinfoseqinrshinyshinyFilessnowsourcetoolsspSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXMLxtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Extract protein motifs form a file in PSA format | extractProteinMotifs |
| Extract sequence fragments from a list of sequences | extractSegments |
| Create a pie chart showing protein motif distribution | freqPie |
| Convert GFF to a binary occurrence matrix | gff2matrix |
| Generate a heatmap from a matrix | matrix2hm |
| Generate a square heatmap from a matrix | matrixToSquareHeatmap |
| Convert PROSITE format to a GFF-like Data Frame | readProsite |
| Parse a PSA (PROSITE Scan ASCII) File | readPsa |
| Launch the PMScanR Shiny Application | runPMScanRShiny |
| Run PS-Scan with Caching and Improved Execution | runPsScan |
