Package: genoPlotR 0.8.11
Lionel Guy
genoPlotR: Plot Publication-Grade Gene and Genome Maps
Draws gene or genome maps and comparisons between these, in a publication-grade manner. Starting from simple, common files, it will draw postscript or PDF files that can be sent as such to journals.
Authors:
genoPlotR_0.8.11.tar.gz
genoPlotR_0.8.11.zip(r-4.5)genoPlotR_0.8.11.zip(r-4.4)genoPlotR_0.8.11.zip(r-4.3)
genoPlotR_0.8.11.tgz(r-4.4-any)genoPlotR_0.8.11.tgz(r-4.3-any)
genoPlotR_0.8.11.tar.gz(r-4.5-noble)genoPlotR_0.8.11.tar.gz(r-4.4-noble)
genoPlotR_0.8.11.tgz(r-4.4-emscripten)genoPlotR_0.8.11.tgz(r-4.3-emscripten)
genoPlotR.pdf |genoPlotR.html✨
genoPlotR/json (API)
NEWS
| # Install 'genoPlotR' in R: |
| install.packages('genoPlotR', repos = c('https://r-forge.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://r-forge.r-project.org/projects/genoplotr
- barto - Comparison of 4 Bartonella genomes
- bbone - Mauve backbone of 4 Bartonella genomes
- chrY_subseg - Comparisons of subsegments of the Y chromosome in human and chimp
- comparisons - Three genes data set
- dna_segs - Three genes data set
Last updated 4 years agofrom:dc8e1d95b3. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 13 2024 |
| R-4.5-win | NOTE | Aug 13 2024 |
| R-4.5-linux | NOTE | Aug 13 2024 |
| R-4.4-win | NOTE | Aug 13 2024 |
| R-4.4-mac | NOTE | Aug 13 2024 |
| R-4.3-win | OK | Aug 13 2024 |
| R-4.3-mac | OK | Aug 13 2024 |
Exports:annotationapply_color_schemeartemisColorsas.annotationas.comparisonas.dna_segas.seg_plotauto_annotatec.dna_segcomparisondna_seggene_typeshuman_ntis.annotationis.comparisonis.dna_segis.seg_plotmiddleplot_gene_maprange.annotationrange.comparisonrange.dna_segread_comparison_from_blastread_comparison_from_tabread_dna_seg_from_emblread_dna_seg_from_fastaread_dna_seg_from_fileread_dna_seg_from_genbankread_dna_seg_from_pttread_dna_seg_from_tabread_mauve_backbonereverseseg_plottrimtrim.seg_plot
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Plot Publication-Grade Gene and Genome Maps | genoPlotR-package genoPlotR |
| Annotation class and class functions | annotation as.annotation is.annotation |
| Apply a color scheme | apply_color_scheme |
| Artemis Colors | artemisColors |
| Auto-annotate dna_segs | auto_annotate |
| Comparison of 4 Bartonella genomes | barto |
| Concatenate dna_seg objects | c.dna_seg |
| Comparisons of subsegments of the Y chromosome in human and chimp | chrY_subseg |
| Comparison class and class functions | as.comparison comparison is.comparison |
| DNA segment (dna_seg) class and class functions | as.dna_seg dna_seg is.dna_seg |
| Gene types | gene_types |
| Human-readable nucleotide scale | human_nt |
| Mauve backbone of 4 Bartonella genomes | bbone mauve_bbone |
| Middles of a dna_seg | middle |
| Plot gene and genome maps | plot_gene_map |
| Range calculation | range.annotation range.comparison range.dna_seg |
| Reading functions | read_comparison_from_blast read_comparison_from_tab read_dna_seg_from_embl read_dna_seg_from_fasta read_dna_seg_from_file read_dna_seg_from_genbank read_dna_seg_from_ptt read_dna_seg_from_tab read_functions read_mauve_backbone |
| Reverse objects | reverse reverse.comparison reverse.default reverse.dna_seg |
| seg_plot class and class functions | as.seg_plot is.seg_plot seg_plot |
| Three genes data set | comparisons dna_segs three_genes |
| Trimming data frames or more complex objects with >= 2 numeric columns | trim trim.annotation trim.comparison trim.default trim.dna_seg trim.seg_plot |
