weblogo
scanpy
weblogo | scanpy | |
---|---|---|
2 | 5 | |
135 | 1,763 | |
1.5% | 2.0% | |
3.7 | 9.3 | |
2 months ago | 5 days ago | |
Python | Python | |
GNU General Public License v3.0 or later | BSD 3-clause "New" or "Revised" License |
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.
weblogo
-
Using MEME general motif finder for splice site consensus?
To get the consensus of splice motifs I usually don't do motif discovery, because I already know where the motif is supposed to be. Instead, I get a window around the splice sites, extract the sequences and collect them in a fasta file. Then I upload the sequences in weblogo to visualize the sequence logo.
-
Amino acid alignment to find shared motifs
you can use this on the comnand line to make nice sequence logos: https://github.com/WebLogo/weblogo
scanpy
- Renaming Genes for Scanpy Plot
- Useful Python Decorators for Data Scientists
-
[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?
-
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.
-
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.
What are some alternatives?
Biopython - Official git repository for Biopython (originally converted from CVS)
scikit-learn - scikit-learn: machine learning in Python
dash - Data Apps & Dashboards for Python. No JavaScript Required.
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.
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
pagoda2 - R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
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.
reloadium - Hot Reloading and Profiling for Python