From bcdcefd3e5675f746795e94d30b0fdd62fade899 Mon Sep 17 00:00:00 2001 From: geertvangeest Date: Sun, 6 Oct 2024 01:40:09 +0000 Subject: [PATCH] auto-generated readme --- README.md | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 52 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 106afdb..f8212fe 100644 --- a/README.md +++ b/README.md @@ -34,6 +34,7 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [C/C++](#c/c++) - [Rust](#rust) - [SPARQL](#sparql) + - [LaTeX](#latex) - [Computational methods and pipelines](#computational-methods-and-pipelines) - [Containerization](#containerization) - [Galaxy](#galaxy) @@ -70,6 +71,7 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [Data science](#data-science) - [Statistics](#statistics) - [Machine learning](#machine-learning) + - [Artificial intelligence](#artificial-intelligence) - [Others](#others) - [General](#general) @@ -84,11 +86,13 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**Gerard Capes** gcapes/git-course](https://github.com/gcapes/git-course) | [website](http://gcapes.github.io/git-course/) - [**carpentries-incubator** carpentries-incubator/gitlab-novice](https://github.com/carpentries-incubator/gitlab-novice) | [website](https://carpentries-incubator.github.io/gitlab-novice/) - [**Data Carpentry** datacarpentry/rr-version-control](https://github.com/datacarpentry/rr-version-control) | [website](http://www.datacarpentry.org/rr-version-control/) -- [**VIB Technologies: Bioinformatics and software projects** vibbits/introduction-github](https://github.com/vibbits/introduction-github) +- [**VIB Technologies: Training material and software projects** vibbits/introduction-github](https://github.com/vibbits/introduction-github) - [**NBIS - National Bioinformatics Infrastructure Sweden** NBISweden/module-versioning-dm-practices](https://github.com/NBISweden/module-versioning-dm-practices/) | [website](https://nbisweden.github.io/module-versioning-dm-practices/) - [**Sergio Martínez Cuesta** semacu/20190927_IntroductionGithub_HDRUK](https://github.com/semacu/20190927_IntroductionGithub_HDRUK) - [**Sergio Martínez Cuesta** semacu/20181003_Intro_git_GitHub](https://github.com/semacu/20181003_Intro_git_GitHub) - [**Sergio Martínez Cuesta** semacu/20171024_GitHub_Chemistry_Cambridge](https://github.com/semacu/20171024_GitHub_Chemistry_Cambridge) +- [**jhudsl** jhudsl/Adv_Reproducibility_in_Cancer_Informatics](https://github.com/jhudsl/Adv_Reproducibility_in_Cancer_Informatics) | [website](https://jhudatascience.org/Adv_Reproducibility_in_Cancer_Informatics) +- [**posit::conf(2024)** posit-conf-2024/dev-ops](https://github.com/posit-conf-2024/dev-ops) ### Unix/Linux @@ -122,7 +126,7 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**SIB Swiss Institute of Bioinformatics** sib-swiss/first-steps-with-python-training](https://github.com/sib-swiss/first-steps-with-python-training) - [**SIB Swiss Institute of Bioinformatics** sib-swiss/intermediate-python-training](https://github.com/sib-swiss/intermediate-python-training) - [**Software Carpentry** swcarpentry/python-novice-inflammation](https://github.com/swcarpentry/python-novice-inflammation) | [website](http://swcarpentry.github.io/python-novice-inflammation/) -- [**VIB Technologies: Bioinformatics and software projects** vibbits/gentle-hands-on-python](https://github.com/vibbits/gentle-hands-on-python) +- [**VIB Technologies: Training material and software projects** vibbits/gentle-hands-on-python](https://github.com/vibbits/gentle-hands-on-python) - [**Talk Python** talkpython/python-for-absolute-beginners-course](https://github.com/talkpython/python-for-absolute-beginners-course) | [website](https://training.talkpython.fm/courses/explore_beginners/python-for-absolute-beginners) - [**Sundeep Agarwal** learnbyexample/py_regular_expressions](https://github.com/learnbyexample/py_regular_expressions) | [website](https://learnbyexample.github.io/py_regular_expressions/) - [**Sundeep Agarwal** learnbyexample/100_page_python_intro](https://github.com/learnbyexample/100_page_python_intro) | [website](https://learnbyexample.github.io/100_page_python_intro/) @@ -167,6 +171,9 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**Python Packages** py-pkgs/py-pkgs](https://github.com/py-pkgs/py-pkgs) | [website](https://py-pkgs.org) - [**bioinfo-prog** bioinfo-prog/cours-python](https://github.com/bioinfo-prog/cours-python) | [website](https://python.sdv.u-paris.fr) - [**R. Burke Squires** burkesquires/python_biologist](https://github.com/burkesquires/python_biologist) +- [**Sergio Martínez Cuesta** semacu/data-science-python](https://github.com/semacu/data-science-python) +- [**MolSSI Education** MolSSI-Education/python_scripting_cms](https://github.com/MolSSI-Education/python_scripting_cms) | [website](https://molssi-education.github.io/python_scripting_cms) +- [**Jean de Dieu Nyandwi** Nyandwi/PythonBasics](https://github.com/Nyandwi/PythonBasics) ### R @@ -326,6 +333,19 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**Sophie Lee** sophie-a-lee/Introduction_R_Tidyverse_course](https://github.com/sophie-a-lee/Introduction_R_Tidyverse_course) | [website](https://introduction-r-tidyverse.netlify.app) - [**Sophie Lee** sophie-a-lee/introduction_rstudio_dluch](https://github.com/sophie-a-lee/introduction_rstudio_dluch) | [website](https://intro-r-dluch.netlify.app) - [**Stephen Turner** stephenturner/workshops](https://github.com/stephenturner/workshops) | [website](http://stephenturner.github.io/workshops) +- [**Fred Hutch Data Science Lab** fhdsl/Tools_for_Reproducible_Workflows_in_R](https://github.com/fhdsl/Tools_for_Reproducible_Workflows_in_R) | [website](https://hutchdatascience.org/Tools_for_Reproducible_Workflows_in_R/) +- [**Aditya Dahiya** Aditya-Dahiya/ggplot2book3e](https://github.com/Aditya-Dahiya/ggplot2book3e/) +- [**posit::conf(2024)** posit-conf-2024/arrow](https://github.com/posit-conf-2024/arrow) | [website](https://posit-conf-2024.github.io/arrow/) +- [**posit::conf(2024)** posit-conf-2024/ds-workflows-r](https://github.com/posit-conf-2024/ds-workflows-r) | [website](https://posit-conf-2024.github.io/ds-workflows-r/) +- [**posit::conf(2024)** posit-conf-2024/databases](https://github.com/posit-conf-2024/databases) | [website](https://pos.it/databases-24) +- [**posit::conf(2024)** posit-conf-2024/pharmaverse](https://github.com/posit-conf-2024/pharmaverse) | [website](https://posit-conf-2024.github.io/pharmaverse/) +- [**posit::conf(2024)** posit-conf-2024/programming-r](https://github.com/posit-conf-2024/programming-r) | [website](https://posit-conf-2024.github.io/programming-r/) +- [**Northwestern IT Research Computing and Data Services** nuitrcs/R-intro-tidyverse-2024](https://github.com/nuitrcs/R-intro-tidyverse-2024) +- [**posit::conf(2024)** posit-conf-2024/tables](https://github.com/posit-conf-2024/tables) +- [**posit::conf(2024)** posit-conf-2024/pkg-dev](https://github.com/posit-conf-2024/pkg-dev) +- [**posit::conf(2024)** posit-conf-2024/r-in-production](https://github.com/posit-conf-2024/r-in-production) +- [**posit::conf(2024)** posit-conf-2024/databricks](https://github.com/posit-conf-2024/databricks) | [website](https://posit-conf-2024.github.io/databricks/) +- [**posit::conf(2024)** posit-conf-2024/wtf](https://github.com/posit-conf-2024/wtf) ### Quarto @@ -335,6 +355,8 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**Hamel Husain** hamelsmu/posit-python-quarto](https://github.com/hamelsmu/posit-python-quarto) | [website](https://bit.ly/pyquarto) - [**Isabella Velásquez** ivelasq/2024-01-23_getting-started-with-report-writing-using-quarto](https://github.com/ivelasq/2024-01-23_getting-started-with-report-writing-using-quarto) | [website](https://ivelasq.quarto.pub/getting-started-with-report-writing-using-quarto/#/title-slide) - [**Julien Roux** julien-roux/SIB_days_2024_workshop_EDI](https://github.com/julien-roux/SIB_days_2024_workshop_EDI/) +- [**posit::conf(2024)** posit-conf-2024/quarto-dashboards](https://github.com/posit-conf-2024/quarto-dashboards) | [website](https://posit-conf-2024.github.io/quarto-dashboards/) +- [**posit::conf(2024)** posit-conf-2024/quarto-websites](https://github.com/posit-conf-2024/quarto-websites) | [website](https://posit-conf-2024.github.io/quarto-websites/) ### Shiny @@ -347,6 +369,9 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**posit-conf-2023** posit-conf-2023/shiny-r-prod](https://github.com/posit-conf-2023/shiny-r-prod) | [website](https://posit-conf-2023.github.io/shiny-r-prod/) - [**ThinkR** ThinkR-open/engineering-shiny-book](https://github.com/ThinkR-open/engineering-shiny-book) | [website](https://engineering-shiny.org) - [**Ted Laderas** laderast/shinyowl](https://github.com/laderast/shinyowl/) | [website](https://laderast.github.io/shinyowl) +- [**posit-dev** posit-dev/intro-to-shiny-for-python](https://github.com/posit-dev/intro-to-shiny-for-python) | [website](https://posit-dev.github.io/intro-to-shiny-for-python/) +- [**posit::conf(2024)** posit-conf-2024/shiny-r-intro](https://github.com/posit-conf-2024/shiny-r-intro) | [website](https://posit-conf-2024.github.io/shiny-r-intro/) +- [**posit::conf(2024)** posit-conf-2024/level-up-shiny](https://github.com/posit-conf-2024/level-up-shiny) | [website](https://posit-conf-2024.github.io/level-up-shiny/) ### Julia @@ -408,6 +433,10 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**Department of Bioinformatics - BiGCaT** BiGCAT-UM/SPARQLTutorialBioSB2019](https://github.com/bigcat-um/SPARQLTutorialBioSB2019) - [**SIB Swiss Institute of Bioinformatics** sib-swiss/SPARQL_course](https://github.com/sib-swiss/SPARQL_course) +### LaTeX + +- [**Fred Hutch Data Science Lab** fhdsl/Overleaf_and_LaTeX_for_Scientific_Articles](https://github.com/fhdsl/Overleaf_and_LaTeX_for_Scientific_Articles) | [website](https://hutchdatascience.org/Overleaf_and_LaTeX_for_Scientific_Articles/) + ## Computational methods and pipelines @@ -433,6 +462,7 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**carpentries-incubator** carpentries-incubator/lesson-gpu-programming](https://github.com/carpentries-incubator/lesson-gpu-programming) | [website](https://carpentries-incubator.github.io/lesson-gpu-programming/) - [**PerMedCoE** PerMedCoE/cluster-tutorial](https://github.com/permedcoe/cluster-tutorial) - [**George G. Vega Yon** gvegayon/appliedhpcr](https://github.com/gvegayon/appliedhpcr) +- [**jhudsl** jhudsl/Computing_for_Cancer_Informatics](https://github.com/jhudsl/Computing_for_Cancer_Informatics) | [website](https://jhudatascience.org/Computing_for_Cancer_Informatics) ### Workflows @@ -447,11 +477,12 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**carpentries-incubator** carpentries-incubator/workflows-snakemake](https://github.com/carpentries-incubator/workflows-snakemake) | [website](https://carpentries-incubator.github.io/workflows-snakemake/) - [**Sateesh_Peri** sateeshperi/nextflow_varcal](https://github.com/sateeshperi/nextflow_varcal) | [website](https://sateeshperi.github.io/nextflow_varcal/nextflow/) - [**Seqera** nextflow-io/training](https://github.com/seqeralabs/nf-training-public) | [website](https://training.nextflow.io) -- [**VIB Technologies: Bioinformatics and software projects** vibbits/nextflow-workshop](https://github.com/vibbits/nextflow-workshop) +- [**VIB Technologies: Training material and software projects** vibbits/nextflow-workshop](https://github.com/vibbits/nextflow-workshop) - [**SIB Swiss Institute of Bioinformatics** sib-swiss/containers-snakemake-training](https://github.com/sib-swiss/containers-snakemake-training) | [website](https://sib-swiss.github.io/containers-snakemake-training/) - [**carpentries-incubator** carpentries-incubator/cwl-novice-tutorial](https://github.com/carpentries-incubator/cwl-novice-tutorial) | [website](https://carpentries-incubator.github.io/cwl-novice-tutorial/) - [**Romain Feron** RomainFeron/workshop-snakemake-sibdays2022](https://github.com/RomainFeron/workshop-snakemake-sibdays2022) - [**Dockstore** dockstore/bcc2020-training](https://github.com/dockstore/bcc2020-training) +- [**Fred Hutch Data Science Lab** fhdsl/GitHub_Automation_for_Scientists](https://github.com/fhdsl/GitHub_Automation_for_Scientists) | [website](http://hutchdatascience.org/GitHub_Automation_for_Scientists/) ### Image analysis @@ -493,6 +524,7 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**The McDonnell Genome Institute** genome/bfx-workshop](https://github.com/genome/bfx-workshop) - [**rapidspeciation** rapidspeciation/biodiversity_genomics_course](https://github.com/rapidspeciation/biodiversity_genomics_course) - [**Applied Genomics** Applied-Genomics-UTD/docs](https://github.com/Applied-Genomics-UTD/docs) +- [**Fred Hutch Data Science Lab** fhdsl/Choosing_Genomics_Tools](https://github.com/fhdsl/Choosing_Genomics_Tools) | [website](http://hutchdatascience.org/Choosing_Genomics_Tools/) ### Next generation sequencing @@ -527,6 +559,7 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**Computational Biology and Bioinformatics at UCLouvain** UCLouvain-CBIO/WSBIM2122](https://github.com/UCLouvain-CBIO/WSBIM2122) | [website](https://uclouvain-cbio.github.io/WSBIM2122/) - [**Saez Lab** saezlab/transcriptutorial](https://github.com/saezlab/transcriptutorial) | [website](https://saezlab.github.io/transcriptutorial/) - [**The Gulbenkian Training Programme in Bioinformatics** GTPB/ADER19F](https://github.com/gtpb/ADER19F) | [website](http://gtpb.github.io/ADER19F) +- [**Khushbu Patel** kpatel427/YouTubeTutorials](https://github.com/kpatel427/YouTubeTutorials) ### RNA-seq @@ -587,6 +620,7 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**UC Davis Bioinformatics Core Training Page** ucdavis-bioinformatics-training/2020-Variant_Analysis_Workshop](https://github.com/ucdavis-bioinformatics-training/2020-Variant_Analysis_Workshop) - [**UC Davis Bioinformatics Core Training Page** ucdavis-bioinformatics-training/2021-July-Genome-Wide-Association-Studies](https://github.com/ucdavis-bioinformatics-training/2021-July-Genome-Wide-Association-Studies) - [**Nina Overgaard Therkildsen** nt246/lcwgs-guide-tutorial](https://github.com/nt246/lcwgs-guide-tutorial) +- [**Dipannita Ghosh** digo4/Clinical-Genomics](https://github.com/digo4/Clinical-Genomics) ### ChIP-seq @@ -700,7 +734,7 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**ELIXIR-Norway Training** ELIXIR-Norway-Training/DMP-writing-workshop](https://github.com/ELIXIR-Norway-Training/DMP-writing-workshop) | [website](https://zenodo.org/doi/10.5281/zenodo.3693710) - [**OpenSciency** opensciency/sprint-content](https://github.com/opensciency/sprint-content) | [website](https://opensciency.github.io/sprint-content/) - [**SIB Swiss Institute of Bioinformatics** sib-swiss/ena-seqdata-training](https://github.com/sib-swiss/ena-seqdata-training) | [website](https://sib-swiss.github.io/ena-seqdata-training/) -- [**VIB Technologies: Bioinformatics and software projects** vibbits/rdm-introductory-course](https://github.com/vibbits/rdm-introductory-course) +- [**VIB Technologies: Training material and software projects** vibbits/rdm-introductory-course](https://github.com/vibbits/rdm-introductory-course) - [**Utrecht University** UtrechtUniversity/dataprivacyhandbook](https://github.com/utrechtuniversity/dataprivacyhandbook) | [website](https://utrechtuniversity.github.io/dataprivacyhandbook/) - [**NBIS - National Bioinformatics Infrastructure Sweden** NBISweden/module-dmp-dm-practices](https://github.com/NBISweden/module-dmp-dm-practices/) | [website](https://nbisweden.github.io/module-dmp-dm-practices/) - [**NBIS - National Bioinformatics Infrastructure Sweden** NBISweden/module-data-publication-dm-practices](https://github.com/NBISweden/module-data-publication-dm-practices/) | [website](https://nbisweden.github.io/module-data-publication-dm-practices/) @@ -711,6 +745,8 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**SIB Swiss Institute of Bioinformatics** sib-swiss/Introduction-FAIR-RDM-DMP](https://github.com/sib-swiss/Introduction-FAIR-RDM-DMP) | [website](https://sib-swiss.github.io/Introduction-FAIR-RDM-DMP/) - [**BioData.pt** BioData-PT/Ready4BioDataManagement](https://github.com/BioData-PT/Ready4BioDataManagement) | [website](https://biodata.pt/training/programmes/r4bdm) - [**posit-conf-2023** posit-conf-2023/managing-os-project](https://github.com/posit-conf-2023/managing-os-project) | [website](https://posit-conf-2023.github.io/managing-os-project/) +- [**Fred Hutch Data Science Lab** fhdsl/Ethical_Data_Handling_for_Cancer_Research](https://github.com/fhdsl/Ethical_Data_Handling_for_Cancer_Research) | [website](https://hutchdatascience.org/Ethical_Data_Handling_for_Cancer_Research/) +- [**Fred Hutch Data Science Lab** fhdsl/NIH_Data_Sharing](https://github.com/fhdsl/NIH_Data_Sharing) | [website](https://hutchdatascience.org/NIH_Data_Sharing/) ### FAIR data @@ -737,6 +773,8 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**SIB Swiss Institute of Bioinformatics** sib-swiss/reproducible-analysis-training](https://github.com/sib-swiss/reproducible-analysis-training) | [website](https://sib-swiss.github.io/reproducible-analysis-training/) - [**ELIXIR Europe Training** elixir-europe-training/ELIXIR-TrP-ContainersPython-CodeRep](https://github.com/elixir-europe-training/ELIXIR-TrP-ContainersPython-CodeRep) | [website](https://elixir-europe-training.github.io/ELIXIR-TrP-ContainersPython-CodeRep/) - [**ELIXIR Europe Training** elixir-europe-training/ELIXIR-TrP-LiterateProgrammingR-CodeRep](https://github.com/elixir-europe-training/ELIXIR-TrP-LiterateProgrammingR-CodeRep) | [website](https://elixir-europe-training.github.io/ELIXIR-TrP-LiterateProgrammingR-CodeRep/) +- [**jhudsl** jhudsl/Reproducibility_in_Cancer_Informatics](https://github.com/jhudsl/Reproducibility_in_Cancer_Informatics) | [website](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/) +- [**jhudsl** jhudsl/Documentation_and_Usability](https://github.com/jhudsl/Documentation_and_Usability) | [website](https://jhudatascience.org/Documentation_and_Usability/) ## Statistics and machine learning @@ -824,9 +862,16 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**posit-conf-2023** posit-conf-2023/python-modeling](https://github.com/posit-conf-2023/python-modeling) - [**Emil Hvitfeldt** EmilHvitfeldt/smltar](https://github.com/EmilHvitfeldt/smltar) | [website](https://smltar.com) - [**Navid Nobani** Naviden/ML-intro-with-Python](https://github.com/Naviden/ML-intro-with-Python) -- [**Maxime Labonne** mlabonne/llm-course](https://github.com/mlabonne/llm-course) | [website](https://mlabonne.github.io/blog/) - [**mlr-org** mlr-org/mlr3book](https://github.com/mlr-org/mlr3book) | [website](https://mlr3book.mlr-org.com) - [**Inria** INRIA/scikit-learn-mooc](https://github.com/INRIA/scikit-learn-mooc) | [website](https://inria.github.io/scikit-learn-mooc) +- [**posit::conf(2024)** posit-conf-2024/vetiver](https://github.com/posit-conf-2024/vetiver) | [website](https://posit-conf-2024.github.io/vetiver/) +- [**posit::conf(2024)** posit-conf-2024/ml-python](https://github.com/posit-conf-2024/ml-python) | [website](https://posit-conf-2024.github.io/ml-python/) + +### Artificial intelligence + +- [**Maxime Labonne** mlabonne/llm-course](https://github.com/mlabonne/llm-course) | [website](https://mlabonne.github.io/blog/) +- [**Fred Hutch Data Science Lab** fhdsl/AI_for_Decision_Makers](https://github.com/fhdsl/AI_for_Decision_Makers) | [website](https://hutchdatascience.org/AI_for_Decision_Makers/) +- [**Fred Hutch Data Science Lab** fhdsl/AI_for_Efficient_Programming](https://github.com/fhdsl/AI_for_Efficient_Programming) | [website](https://hutchdatascience.org/AI_for_Efficient_Programming/) ## Others @@ -859,3 +904,5 @@ Below you'll find a curated list of **bioinformatics training material**. All ma - [**Sex Chromosome Lab** SexChrLab/BioinformaticsIntroduction](https://github.com/SexChrLab/BioinformaticsIntroduction/) - [**Harvard Informatics** harvardinformatics/learning-bioinformatics-at-home](https://github.com/harvardinformatics/learning-bioinformatics-at-home) - [**gladstone-institutes** gladstone-institutes/Bioinformatics-Workshops](https://github.com/gladstone-institutes/Bioinformatics-Workshops/) | [website](https://github.com/gladstone-institutes/Bioinformatics-Presentations/wiki) +- [**jhudsl** jhudsl/Informatics_Research_Leadership](https://github.com/jhudsl/Informatics_Research_Leadership) | [website](https://jhudatascience.org/Informatics_Research_Leadership/) +- [**Pachter Lab** pachterlab/BI-BE-CS-183-2023](https://github.com/pachterlab/BI-BE-CS-183-2023)