Package: G4SNVHunter 0.99.4
Rongxin Zhang
G4SNVHunter: Evaluating SNV-Induced Disruption of G-Quadruplex Structures
G-quadruplexes (G4s) are unique nucleic acid secondary structures predominantly found in guanine-rich regions and have been shown to be involved in various biological regulatory processes. G4SNVHunter is an R package designed to rapidly identify genomic sequences with G4-forming potential and accurately screen user-provided single nucleotide variants (also applicable to single nucleotide polymorphisms) that may destabilize these structures. This enables users to screen key variants for further experimental study, investigating how these variants may influence biological functions, such as gene regulation, by altering G4 formation.
Authors:
G4SNVHunter_0.99.4.tar.gz
G4SNVHunter_0.99.4.zip(r-4.5)G4SNVHunter_0.99.4.zip(r-4.4)G4SNVHunter_0.99.4.zip(r-4.3)
G4SNVHunter_0.99.4.tgz(r-4.4-x86_64)G4SNVHunter_0.99.4.tgz(r-4.4-arm64)G4SNVHunter_0.99.4.tgz(r-4.3-x86_64)G4SNVHunter_0.99.4.tgz(r-4.3-arm64)
G4SNVHunter_0.99.4.tar.gz(r-4.5-noble)G4SNVHunter_0.99.4.tar.gz(r-4.4-noble)
G4SNVHunter_0.99.4.tgz(r-4.4-emscripten)G4SNVHunter_0.99.4.tgz(r-4.3-emscripten)
G4SNVHunter.pdf |G4SNVHunter.html✨
G4SNVHunter/json (API)
NEWS
| # Install 'G4SNVHunter' in R: |
| install.packages('G4SNVHunter', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rongxinzh/g4snvhunter/issues
On BioConductor:G4SNVHunter-0.99.4(bioc 3.21)
Last updated 1 months agofrom:73edf5ef51. Checks:4 OK, 5 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 13 2025 |
| R-4.5-win-x86_64 | NOTE | Jan 13 2025 |
| R-4.5-linux-x86_64 | NOTE | Jan 13 2025 |
| R-4.4-win-x86_64 | NOTE | Jan 13 2025 |
| R-4.4-mac-x86_64 | NOTE | Jan 13 2025 |
| R-4.4-mac-aarch64 | NOTE | Jan 13 2025 |
| R-4.3-win-x86_64 | OK | Jan 13 2025 |
| R-4.3-mac-x86_64 | OK | Jan 13 2025 |
| R-4.3-mac-aarch64 | OK | Jan 13 2025 |
Exports:checkSNVfilterSNVImpactG4HunterDetectG4HunterScoreloadSequenceplotG4InfoplotImpactSeqplotSNVImpactSNVImpactG4
Dependencies:askpassBiocGenericsBiostringsclicolorspacecowplotcrayoncurldata.tablefansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpointdensityggseqlogogluegridExtragtablehmshttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigprettyunitsprogressR6RColorBrewerRcppRcppRollrlangS4VectorsscalessystibbleUCSC.utilsutf8vctrsviridisviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Check the validity of SNVs | checkSNV |
| Filter SNV Impact GRanges Object Based on User-Defined Thresholds | filterSNVImpact |
| Detect G4 Sequences Using G4Hunter Algorithm | G4HunterDetect |
| Calculate the G4Hunter Score for a Given Sequence | G4HunterScore |
| Load Genome Sequences | loadSequence |
| Plot Basic Statistics of G4s Detected by the G4HunterDetect Function | plotG4Info |
| Visualize the variants in G4 sequence | plotImpactSeq |
| Plot the Impact of SNVs on G4Hunter Scores | plotSNVImpact |
| Single Nucleotide Polymorphisms GRanges Object | snp_gr |
| Single Nucleotide Variant GRanges Object | snv_gr |
| Evaluate the Impact of SNVs on G4 Sequences | SNVImpactG4 |
