Package: geneviewer 0.1.11

geneviewer: Gene Cluster Visualizations

Provides tools for plotting gene clusters and transcripts by importing data from GenBank, FASTA, and GFF files. It performs BLASTP and MUMmer alignments [Altschul et al. (1990) <doi:10.1016/S0022-2836(05)80360-2>; Delcher et al. (1999) <doi:10.1093/nar/27.11.2369>] and displays results on gene arrow maps. Extensive customization options are available, including legends, labels, annotations, scales, colors, tooltips, and more.

Authors:Niels van der Velden [aut, cre]

geneviewer_0.1.11.tar.gz
geneviewer_0.1.11.zip(r-4.7)geneviewer_0.1.11.zip(r-4.6)geneviewer_0.1.11.zip(r-4.5)
geneviewer_0.1.11.tgz(r-4.6-any)geneviewer_0.1.11.tgz(r-4.5-any)
geneviewer_0.1.11.tar.gz(r-4.7-any)geneviewer_0.1.11.tar.gz(r-4.6-any)
geneviewer_0.1.11.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
geneviewer/json (API)

# Install 'geneviewer' in R:
install.packages('geneviewer', repos = c('https://nvelden.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nvelden/geneviewer/issues

Datasets:

On CRAN:

Conda:

genetics

5.93 score 99 stars 34 scripts 352 downloads 34 exports 42 dependencies

Last updated from:edae299b04. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK156
source / vignettesOK184
linux-release-x86_64OK184
macos-release-arm64OK106
macos-oldrel-arm64OK99
windows-develOK115
windows-releaseOK99
windows-oldrelOK97
wasm-releaseOK160

Exports:%>%gbk_features_to_dfGC_alignGC_annotationGC_chartGC_chartOutputGC_clusterGC_clusterFooterGC_clusterLabelGC_clusterTitleGC_colorGC_coordinatesGC_genesGC_gridGC_labelsGC_legendGC_linksGC_normalizeGC_scaleGC_scaleBarGC_sequenceGC_titleGC_tooltipGC_trackMouseGC_transcriptgenbank_to_fastaget_intronsmummer_alignmentprotein_blastread_bedread_fastaread_gbkread_gffrenderGC_chart

Dependencies:base64encbslibcachemclicpp11digestdplyrevaluatefastmapfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmemoisemimepillarpkgconfigpurrrR6rappdirsrlangrmarkdownsassstringistringrtibbletidyrtidyselecttinytexutf8vctrswithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
BRCA1 Splice VariantsBRCA1_splice_variants
Erythromycin BlastP resultserythromycin_BlastP
Erythromycin Gene Cluster Dataerythromycin_cluster
Convert GenBank Features to Data Framegbk_features_to_df
Align gene clustersGC_align
Add Annotations to a GC_chartGC_annotation
Create a GC Chart VisualizationGC_chart
Modify Cluster SettingsGC_cluster
Add a Footer to Each Cluster in a GC ChartGC_clusterFooter
Set or Update Cluster Labels for a GC ChartGC_clusterLabel
Update cluster Title of a GC Chart ClusterGC_clusterTitle
Update Color Scheme in Gene ChartGC_color
Modify Coordinates in a GC ChartGC_coordinates
Modify Gene Characteristics within a ChartGC_genes
Update Grid Display of a GC Chart ClusterGC_grid
Add Labels to Each Cluster in a GC ChartGC_labels
Set Legend for a Gene ChartGC_legend
Add Links to GC ChartGC_links
Normalize Gene Clusters in a Genomic ChartGC_normalize
Update Scale of a GC Chart ClusterGC_scale
Update Scale Bar of a GC Chart ClusterGC_scaleBar
Update Sequence Display of a GC Chart ClusterGC_sequence
Add Title to a GC_chartGC_title
Set Tooltip for a Gene ChartGC_tooltip
Track Mouse Movement in a GC_chartGC_trackMouse
Modify Transcript Characteristics within a ChartGC_transcript
Convert GenBank to FASTA Formatgenbank_to_fasta
Shiny bindings for geneviewerGC_chartOutput geneviewer-shiny renderGC_chart
Calculate Intron Positions Based on Exonsget_introns
Human Dystrophin Transcripts Datahs_dystrophin_transcripts
Human HOX Gene Cluster Datahuman_hox_genes
Perform Sequence Alignment Using MUMmermummer_alignment
ophA Gene Cluster from Omphalotus oleariusophA_clusters
Perform Protein BLAST Analysis Within Specified Clustersprotein_blast
Read BED Filesread_bed
Read Protein Sequences from FASTA Filesread_fasta
Read Data from GenBank Filesread_gbk
Read GFF Filesread_gff