bracken_plot
A Shiny app for taxonomic abundance visualization (by acvill)
dada2
Accurate sample inference from amplicon data with single nucleotide resolution (by benjjneb)
| bracken_plot | dada2 | |
|---|---|---|
| 2 | 1 | |
| 7 | 491 | |
| - | 1.2% | |
| 5.9 | 6.6 | |
| 12 months ago | 12 days ago | |
| R | R | |
| MIT License | GNU Lesser General Public License v3.0 only |
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.
bracken_plot
Posts with mentions or reviews of bracken_plot.
We have used some of these posts to build our list of alternatives
and similar projects.
- analysis of kraken2 reports
-
Looking for some resources on creating a graph like this. Or the name of a graph like this so I can look up specific resources for R. :)
These are commonly called stacked bar plots or taxa relative abundance plots. You frequently see these plots in microbiome research papers where the authors performed either 16S or metagenomic sequencing. Given the type of data you have, you can use tools that are already available. Take a look at the R source code for this tool, which includes features like color palette recycling and grouping of taxa below a minimum abundance threshold into an “other” category.
dada2
Posts with mentions or reviews of dada2.
We have used some of these posts to build our list of alternatives
and similar projects.
-
Error model generation and subsequent steps in DADA2 pipeline for multiple sequencing runs
It is recommended to process each run separately (https://github.com/benjjneb/dada2/issues/1177). Each flow cell behaves differently, so the error model for one might not work well for another run. You can merge them together once you have your sequence table.
What are some alternatives?
When comparing bracken_plot and dada2 you can also consider the following projects:
timevis - 📅 Create interactive timeline visualizations in R
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
electricShine - Create Standalone Installable Shiny Apps
MicrobiomeStat - Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
regexplain - 🔍 An RStudio addin slash regex utility belt
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite