pagoda2 vs scanpy

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pagoda2		scanpy
	Project
2	Mentions	5
191	Stars	1,757
5.8%	Growth	3.5%
5.3	Activity	9.3
2 months ago	Latest Commit	2 days ago
JavaScript	Language	Python
-	License	BSD 3-clause "New" or "Revised" License

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.

pagoda2

Posts with mentions or reviews of pagoda2. We have used some of these posts to build our list of alternatives and similar projects.

GOterm analysis in Seurat
1 project | /r/bioinformatics | 6 Aug 2022

Try pagoda2 for this: https://github.com/kharchenkolab/pagoda2
Seurat Vs Pagoda2 For Scrnaseq Analysis
1 project | /r/bioinformatics | 4 Jan 2021

I realize that this is a bit old, but I find pagoda2 faster: https://github.com/kharchenkolab/pagoda2

scanpy

Posts with mentions or reviews of scanpy. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-05-23.

Renaming Genes for Scanpy Plot
1 project | /r/bioinformatics | 15 Jun 2023
Useful Python Decorators for Data Scientists
2 projects | news.ycombinator.com | 23 May 2022
[Scanpy] Installation issues related to pytables
1 project | /r/learnpython | 8 Mar 2022

Upon searching stack, I still do not understand the exact issue, as the file "hdf5extension.cp38-win_amd64" is present within C:\Users\username\anaconda3\lib\site-packages\tables\. Would anyone be able to explain the problem and any potential circumventions?
standardize/normalize seq data
1 project | /r/bioinformatics | 17 Jan 2022

I would suggest you explore with SCANPY and verify if your batch labels generate a strong separation in your samples (PCA, tSNE, UMAP). If you then need to correct for batches, according to how simple/complex they are, you can choose a tool from this benchmark.
Flipping one histogram below the axis.
1 project | /r/matlab | 2 Sep 2021

I am plotting 2 1-D histograms on top of one another using a hold on command. Is there a way to have one histogram be upside down, and then to flip the entire plot 90˚? I am looking to create a violin plot https://github.com/theislab/scanpy/issues/1448 on my own, having one histogram on the left, and one on the right.

What are some alternatives?

When comparing pagoda2 and scanpy you can also consider the following projects:

seurat - R toolkit for single cell genomics

scikit-learn - scikit-learn: machine learning in Python

kana - Single cell analysis in the browser

dash - Data Apps & Dashboards for Python. No JavaScript Required.

alevin-fry - 🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

data-science-ipython-notebooks - Data science Python notebooks: Deep learning (TensorFlow, Theano, Caffe, Keras), scikit-learn, Kaggle, big data (Spark, Hadoop MapReduce, HDFS), matplotlib, pandas, NumPy, SciPy, Python essentials, AWS, and various command lines.

too-many-cells - Cluster single cells and analyze cell clade relationships with colorful visualizations.

deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

dash-cytoscape - Interactive network visualization in Python and Dash, powered by Cytoscape.js

getting-started-with-genomics-tools-and-resources - Unix, R and python tools for genomics and data science

Keras - Deep Learning for humans

Ray - Ray is a unified framework for scaling AI and Python applications. Ray consists of a core distributed runtime and a set of AI Libraries for accelerating ML workloads.