diff --git a/README.md b/README.md index 042fb3027d56013457edd58c68fceaa430a056d2..8116c1a15b61943a17c52de81c56640386ad530b 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>