ggtranscript
Visualizing transcript structure and annotation using ggplot2 (by dzhang32)
gggenomes
A grammar of graphics for comparative genomics (by thackl)
| ggtranscript | gggenomes | |
|---|---|---|
| 1 | 3 | |
| 118 | 561 | |
| - | - | |
| 10.0 | 8.6 | |
| almost 2 years ago | 3 months ago | |
| R | R | |
| GNU General Public License v3.0 or later | GNU General Public License v3.0 or later |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
ggtranscript
Posts with mentions or reviews of ggtranscript.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-03-03.
-
representing gene/transcript layout with variants, suitable approaches?
https://github.com/dzhang32/ggtranscript and https://github.com/kauralasoo/wiggleplotr look like good starting points, and since they output ggplot objects you can add some layers (like geom_segment or other geometries, and ggrepel for labels) to annotate them. Otherwise you can go the "from scratch" route using ggplot with some polygons and segments.
gggenomes
Posts with mentions or reviews of gggenomes.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-09-10.
-
Software to make in-scale illustrations of genomic locations
If you’re R proficient, gggenomes: https://github.com/thackl/gggenomes
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pyGenomeViz: A genome visualization python package for comparative genomics
In R, there are a wide variety of packages that provide APIs for genome visualization, such as genoPlotR and gggenomes.
- Whole genome synteny plots
What are some alternatives?
When comparing ggtranscript and gggenomes you can also consider the following projects:
ggpointdensity - :chart_with_upwards_trend: :bar_chart: Introduces geom_pointdensity(): A Cross Between a Scatter Plot and a 2D Density Plot.
gggenes - ➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2
pyGenomeViz - A genome visualization python package for comparative genomics
gganimate - A Grammar of Animated Graphics
orthologr - Genome wide orthology inference and dNdS estimation
Synima - Synteny Imager
patchwork - The Composer of ggplots
redotable - A dotplot application for DNA/RNA sequence
DnaFeaturesViewer - :eye: Python library to plot DNA sequence features (e.g. from Genbank files)
calendR - Ready to print calendars with ggplot2