scanpy
getting-started-with-genomics-tools-and-resources
| scanpy | getting-started-with-genomics-tools-and-resources | |
|---|---|---|
| 5 | 2 | |
| 1,757 | 1,101 | |
| 1.7% | - | |
| 9.3 | 4.8 | |
| 6 days ago | 22 days ago | |
| Python | Shell | |
| BSD 3-clause "New" or "Revised" License | - |
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scanpy
- Renaming Genes for Scanpy Plot
- Useful Python Decorators for Data Scientists
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[Scanpy] Installation issues related to pytables
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?
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standardize/normalize seq data
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.
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Flipping one histogram below the axis.
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.
getting-started-with-genomics-tools-and-resources
- Does pitt offer any r-programming courses for non-CS majors?
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What are some of the best free software out there for exploratory bioinformaticians / aspiring synthetic biology researchers?
And, a much more comprehensive list of tools from a github contributor: https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources
What are some alternatives?
scikit-learn - scikit-learn: machine learning in Python
manjaro-linux - Shell scripts for setting up Manjaro Linux for Python programming and deep learning
dash - Data Apps & Dashboards for Python. No JavaScript Required.
bioconda-recipes - Conda recipes for the bioconda channel.
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.
biowasm - WebAssembly modules for genomics
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
TeamTeri - Bioinformatics on GCP, AWS or Azure
dash-cytoscape - Interactive network visualization in Python and Dash, powered by Cytoscape.js
metaflow-on-kubernetes-docs - Documentation For Running Metaflow on Kubernetes
pagoda2 - R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets