Introduction | Getting Started | How to run PICB | BAM File Requirements | Information on the demo dataset | Reference Genome | Running PICB | Load Alignments with PICBload | Build piRNA Clusters with PICBbuild | Optimize parameters with PICBoptimize | Strand-specific analysis with PICBstrandanalysis | Explore Results | Export Results | Import Results | Parameter Adjustments | Parameters for PICBload | Parameters for PICBbuild | Output | Metadata Columns | Acknowledgments | Session Information
Package: PICB 1.5.0
Franziska Ahrend
PICB: piRNA Cluster Builder
piRNAs (short for PIWI-interacting RNAs) and their PIWI protein partners play a key role in fertility and maintaining genome integrity by restricting mobile genetic elements (transposons) in germ cells. piRNAs originate from genomic regions known as piRNA clusters. The piRNA Cluster Builder (PICB) is a versatile toolkit designed to identify genomic regions with a high density of piRNAs. It constructs piRNA clusters through a stepwise integration of unique and multimapping piRNAs and offers wide-ranging parameter settings, supported by an optimization function that allows users to test different parameter combinations to tailor the analysis to their specific piRNA system. The output includes extensive metadata columns, enabling researchers to rank clusters and extract cluster characteristics.
Authors:
PICB_1.5.0.tar.gz
PICB_1.5.0.zip(r-4.7)PICB_1.5.0.zip(r-4.6)PICB_1.5.0.zip(r-4.5)
PICB_1.5.0.tgz(r-4.6-any)PICB_1.5.0.tgz(r-4.5-any)
PICB_1.5.0.tar.gz(r-4.7-any)PICB_1.5.0.tar.gz(r-4.6-any)
PICB_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PICB/json (API)
| # Install 'PICB' in R: |
| install.packages('PICB', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/haaselab/picb/issues
On BioConductor:PICB-1.5.0(bioc 3.24)PICB-1.4.0(bioc 3.23)
geneticsgenomeannotationsequencingfunctionalpredictioncoveragetranscriptomics
Last updated from:a70935e5e9. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 216 | ||
| linux-devel-x86_64 | NOTE | 549 | ||
| source / vignettes | OK | 318 | ||
| linux-release-x86_64 | NOTE | 579 | ||
| macos-release-arm64 | NOTE | 503 | ||
| macos-oldrel-arm64 | NOTE | 327 | ||
| windows-devel | NOTE | 527 | ||
| windows-release | NOTE | 523 | ||
| windows-oldrel | NOTE | 515 | ||
| wasm-release | OK | 192 |
Exports:PICBannotatePICBbuildPICBexporttoexcelPICBgetchromosomesPICBimportfromexcelPICBloadPICBloadfastaPICBoptimizePICBstrandanalysis
Dependencies:abindade4BHBiobaseBiocGenericsBiocParallelBiostringsbitopscigarilloclicodetoolscpp11crayondata.tableDelayedArraydplyrformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesglueIRangeslambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsnlmeopenxlsxpillarpixmappkgconfigR6RcppRcppArmadilloRhtslibrlangRsamtoolsS4ArraysS4VectorssegmentedSeqinfoseqinrsnowspSparseArraystringiSummarizedExperimenttibbletidyselectutf8vctrswithrXVectorzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotate GRanges according to a piRNA library | PICBannotate |
| Build piRNA seeds/cores/clusters from alignments | PICBbuild |
| Export cluster object into an Excel file | PICBexporttoexcel |
| Get SeqInfo object from standard non-circular chromosome names from your genome | PICBgetchromosomes |
| Import cluster object from an Excel file | PICBimportfromexcel |
| Load and preprocess BAM files containing piRNA alignments | PICBload |
| Get SeqInfo object from a fasta file | PICBloadfasta |
| Runs PICBbuild multiple times with provided parameters and returns optimization data frame. | PICBoptimize |
| Add sense/antisense ratio of unique piRNAs per piRNA cluster | PICBstrandanalysis |