Package: minimapR 0.0.1.1
minimapR: Wrapper for 'minimap2'
Wrapper for 'Minimap2'. 'Minimap2' is a very valuable long read aligner for the Pacbio and Oxford Nanopore Technologies sequencing platforms. 'minimapR' is an R wrapper for 'minimap2' which was developed by Heng Li <[email protected]>. *SPECIAL NOTES 1. Examples can only be run from 'GitHub' installation. 2. If using a Windows operating system, installation of the 'MSYS2' Linux emulator is required. 3. If using a Mac operating system, installation of 'Homebrew' is required. 4. Git needs to be installed on your system. Li, Heng (2018) <doi:10.1093/bioinformatics/bty191> "Minimap2: pairwise alignment for nucleotide sequences".
Authors:
minimapR_0.0.1.1.tar.gz
minimapR_0.0.1.1.zip(r-4.5)minimapR_0.0.1.1.zip(r-4.4)minimapR_0.0.1.1.zip(r-4.3)
minimapR_0.0.1.1.tgz(r-4.4-any)minimapR_0.0.0.96.tgz(r-4.3-any)
minimapR_0.0.1.1.tar.gz(r-4.5-noble)minimapR_0.0.1.1.tar.gz(r-4.4-noble)
minimapR_0.0.1.1.tgz(r-4.4-emscripten)minimapR_0.0.1.1.tgz(r-4.3-emscripten)
minimapR.pdf |minimapR.html✨
minimapR/json (API)
| # Install 'minimapR' in R: |
| install.packages('minimapR', repos = c('https://jake-bioinfo.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jake-bioinfo/minimapr/issues
Last updated 5 days agofrom:a98b6c3a53. Checks:OK: 5 WARNING: 1 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 18 2024 |
| R-4.5-win | OK | Nov 18 2024 |
| R-4.5-linux | WARNING | Nov 18 2024 |
| R-4.4-win | OK | Nov 18 2024 |
| R-4.4-mac | OK | Nov 18 2024 |
| R-4.3-win | OK | Nov 18 2024 |
| R-4.3-mac | NOTE | Sep 20 2024 |
Exports:clone_repominimap2minimap2_checkminimap2_installationmm2_installsamtools_checksamtools_install
Dependencies:askpassBHBiocGenericsBiocParallelBiostringsbitopsclicodetoolscolorspacecpp11crayoncurldplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpafrpillarpkgconfigR6RColorBrewerRhtslibrlangRsamtoolsS4VectorsscalessnowstringistringrsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Clone a Git repository | clone_repo |
| minimap2 | minimap2 |
| minimap2_check | minimap2_check |
| minimap2_installation | minimap2_installation |
| minimap2_install | mm2_install |
| samtools_check | samtools_check |
| samtools_install | samtools_install |
