To work with LOGAN Search data, see slide 35 of Rayan Chikhi | Project Logan Assembling all public sequencing data | CGSI 2024 (around 20.32 minute mark), need awscli and zst installed
Wayne's Bioinformatics Code Portal fomightez
fomightez
/ demo_ipylab_using_documentsearch.ipynb
Created
May 16, 2025 16:20
Demonstrate using documentsearch in a Jupyter Notebook via ipylab for programmatic text search, in reply to a Jupyter Discourse thread https://discourse.jupyter.org/t/targeted-documentsearch-command/34957?u=fomightez
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fomightez
/ buffons_python2.ipynb
Created
April 8, 2025 16:08
Python 2 version of `Buffons_Needle_Sim.ipynb` from https://nbviewer.org/github/unpingco/Python-for-Signal-Processing/ , see https://discourse.jupyter.org/t/how-to-convert-nb-v3-into-v4-format/34404/2?u=fomightez
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fomightez
/ mre_for_highlight_gene_names.py
Last active
March 31, 2025 20:05
For SO https://stackoverflow.com/q/79546920/8508004 - MRE only. At this time the way the color is made doesn't transfer to Excel. You can color whole cell using `props` and then that would transfer
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| import pandas as pd | |
| import numpy as np | |
| import matplotlib as mpl | |
| import re | |
| df = pd.DataFrame({ | |
| "Gene_name": ["sdsR", "arrS","gadF"], | |
| "Genes_in_same_transcription_unit": ['pphA, sdsR', 'arrS','mdtF, mdtE, gadF, gadE'], | |
| }) | |
| # Convert Gene_name column to a set for quick lookup |
fomightez
/ Plotting_Example_modern_Jupyter.ipynb
Created
March 25, 2025 16:00
How to test plots in modern Jupyther without installing anything or signing up for an account
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fomightez
/ SO79494011-related.ipynb
Last active
March 8, 2025 16:25
In reference to https://stackoverflow.com/a/79494011/8508004 which may be deleted as violating current policy
fomightez
/ nba.ipynb
Created
March 6, 2025 18:48
In relation to [this Jupyter Discourse post](https://discourse.jupyter.org/t/how-to-execute-notebook-in-different-namespace/33532?u=fomightez)
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fomightez
/ test_pyfasma-spc_package_process.ipynb
Created
March 1, 2025 17:07
Test pyfasma-spc package in modern Jupyter and Python for SO https://stackoverflow.com/q/79476297/8508004
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fomightez
/ confusion_matrix_plot_via_seaborn_for_SO.ipynb
Created
February 2, 2025 22:43
confusion matrix plot via seaborn for SO
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fomightez
/ 01_moving_dot.ipynb
Last active
January 6, 2025 21:46
Suggestion for https://github.com/pawjast/code_and_pepper/blob/main/src/animations/01_moving_dot.ipynb
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