From 046effae4b64a7a382be884250cedf8eaaca286a Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 2 Aug 2023 18:04:43 +0200
Subject: [PATCH] More structure, more ressources.

---
 README.md | 106 +++++++++++++++++++++++++++++++++++++++---------------
 1 file changed, 77 insertions(+), 29 deletions(-)

diff --git a/README.md b/README.md
index 042fb30..8116c1a 100644
--- a/README.md
+++ b/README.md
@@ -49,7 +49,35 @@ To parse XML formats.
 URL: <https://www.crummy.com/software/BeautifulSoup/>
 
 
-## Data analysis
+## Graphics
+
+### matplotlib
+
+Base graphics library.
+
+URL: <https://matplotlib.org/>
+
+### seaborn
+
+Built on top of matplotlib, to provide some common graphical representations.
+
+URL: <https://seaborn.pydata.org/>
+
+### plotnine
+
+One of the Python "versions" of ggplot.
+
+URL: <https://plotnine.readthedocs.io/en/stable/index.html>
+
+### pylustrator
+
+To manually adjust matplotlib figures and get the corresponding code.
+I haven't tried it.
+
+URL: <https://pylustrator.readthedocs.io/en/latest/>
+
+
+## General data analysis
 
 ### scipy
 
@@ -75,24 +103,6 @@ General machine learning.
 
 URL: <https://scikit-learn.org/stable/>
 
-### matplotlib
-
-Graphics.
-
-URL: <https://matplotlib.org/>
-
-### seaborn
-
-Built on top of matplotlib, to provide some common graphical representations.
-
-URL: <https://seaborn.pydata.org/>
-
-### plotnine
-
-One of the Python "versions" of ggplot.
-
-URL: <https://plotnine.readthedocs.io/en/stable/index.html>
-
 ### plydata
 
 "dplyr" for pandas.
@@ -112,6 +122,14 @@ I haven't tried it yet as of august 2023.
 
 URL: <https://www.pola.rs/>
 
+### anndata
+
+Another alternative for pandas?
+
+I haven't tried it.
+
+URL: <https://anndata.readthedocs.io/en/latest/>
+
 ### rpy2
 
 I have used it to run functions provided by R packages from Python because programming with R was frustrating.
@@ -119,7 +137,8 @@ However, using rpy2 was not really a pleasant programming experience either.
 
 URL: <https://rpy2.github.io/>
 
-## Bioinfofmatics
+
+## Bioinformatics
 
 ### biopython
 
@@ -170,7 +189,6 @@ Various tools to display "deep" sequencing data. There is a Python API.
 
 URL: <https://deeptools.readthedocs.io/en/develop/index.html>
 
-
 ### pybigwig
 
 To handle bigwig files.
@@ -190,15 +208,30 @@ To perform pairwise sequence alignment.
 
 URL: <https://github.com/jeffdaily/parasail-python>
 
+### scikit-bio
+
+I have used it to handle distance matrices: <http://scikit-bio.org/docs/latest/generated/skbio.stats.distance.html>
+
+URL: <http://scikit-bio.org/>
+
+### scikit-allel
+
+For population genetics.
+
+URL: <https://scikit-allel.readthedocs.io/en/stable/index.html>
+
+
+## Phylogenetics
+
 ### ete
 
-To display phylogenetic trees.
+To display phylogenetic trees. I briefly used it a long time ago.
 
 URL: <http://etetoolkit.org/>
 
 ### dendropy
 
-To manipulate phylogenetic trees.
+To manipulate phylogenetic trees. I briefly used it a long time ago.
 
 URL: <https://dendropy.org/>
 
@@ -208,14 +241,29 @@ Versatile MCMC phylogeny building using Python.
 
 URL: <https://p4.nhm.ac.uk/>
 
-### scikit-bio
 
-I have used it to handle distance matrices: <http://scikit-bio.org/docs/latest/generated/skbio.stats.distance.html>
+## Not a library
 
-URL: <http://scikit-bio.org/>
+### Software Carpentry
 
-### scikit-allel
+I used some of their old material (before 2010) to improve my programming practice in Python.
 
-For population genetics.
+URL: <https://software-carpentry.org/lessons/>
 
-URL: <https://scikit-allel.readthedocs.io/en/stable/index.html>
+### Python charts
+
+A guide to data visualisation using Python.
+
+URL: <https://python-charts.com/>
+
+### The little books of Python anti-patterns
+
+Some programming good practice.
+
+URL: <https://quantifiedcode.github.io/python-anti-patterns/>
+
+### FIDLE
+
+Introduction to deep learning, with an admirable course support based on Jupyter notebooks.
+
+URL: <https://gricad-gitlab.univ-grenoble-alpes.fr/talks/fidle>
-- 
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