seqkit
plotnine
seqkit | plotnine | |
---|---|---|
3 | 36 | |
1,205 | 3,828 | |
- | - | |
8.5 | 9.6 | |
6 days ago | 9 days ago | |
Go | Python | |
MIT License | MIT License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
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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.
seqkit
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A look at the Mojo language for bioinformatics
I've been thinking to learn Rust for these use cases, but always get frustrated with the complexity.
I find Go is a great middle-ground though! And now there starts to be a few more bio-related tools and toolkits out there, including:
- https://github.com/vertgenlab/gonomics
- https://github.com/biogo/biogo
- https://github.com/shenwei356/bio
... except from there being some really popular bio tools written in Go, like:
- https://github.com/shenwei356/seqkit
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Help with understanding awk code
You could also check out tools specialized for FASTA processing like https://github.com/shenwei356/seqkit and https://github.com/lh3/seqtk
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What are some good examples of well-engineered bioinformatics pipelines?
Seqkit - thoroughly maintained with extensive tutorials and benchmarking info - https://github.com/shenwei356/seqkit
plotnine
- FLaNK AI Weekly 18 March 2024
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A look at the Mojo language for bioinformatics
To your last point, have you tried plotnine? It's meant to be ggplot2 for python.
https://github.com/has2k1/plotnine
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Mastering Matplotlib: A Step-by-Step Tutorial for Beginners
plotnine - A grammar of graphics for Python based on ggplot2.
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Top 10 growing data visualization libraries in Python in 2023
Github: https://github.com/has2k1/plotnine
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Lets-Plot: An open-source plotting library by JetBrains
This seems quite similar to plotnine [0], which also provides a grammar of graphics interface for Python. That said, I love ggplot and I can't wait to use this in my research! I hope we can port/re-implement ggthemes, scientificplots [1], and other ggplot libraries for lets-plot.
0: https://plotnine.readthedocs.io/en/stable/
1: https://github.com/garrettj403/SciencePlots
- When would you use R instead of Python?
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[P] Easily make complex plots using ChatGPT [open source]
There is [plotnine](https://plotnine.readthedocs.io/en/stable/) which tries to implement ggplot in Python.
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Is R or Python an EASIER option for non-CS/SE grads?
You could use plotnine if you like the grammar of graphics concept: https://plotnine.readthedocs.io/en/stable/
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Every modeler is supposed to be a great Python programmer
> Python doesn’t yet have anything remotely close to ggplot for rapidly making exploratory graphics, for example.
Plug for plotnine (https://plotnine.readthedocs.io/en/stable/). I don't know R but use ggplot indirectly through this library for exploratory data analysis, and comparing the experience to any other python plotting library, I understand why R folks are usually so sad to be using Python.
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Why has nobody ported ggplot to Python?
They have, https://plotnine.readthedocs.io/en/stable/
What are some alternatives?
seqtk - Toolkit for processing sequences in FASTA/Q formats
seaborn - Statistical data visualization in Python
sage - Proteomics search & quantification so fast that it feels like magic
matplotlib - matplotlib: plotting with Python
rush - A cross-platform command-line tool for executing jobs in parallel
Altair - Declarative statistical visualization library for Python
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
plotly - The interactive graphing library for Python :sparkles: This project now includes Plotly Express!
juicer - A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
ggplot - ggplot port for python
spades - SPAdes Genome Assembler
bokeh - Interactive Data Visualization in the browser, from Python