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Collection of bioinformatics training materials

License: Other

Python 100.00%

training-collection's Introduction

Bioinformatics training materials

Do you like this collection? You're going to love glittr.org! The collection below is still maintained but updated by glittr.org. So, if you have anything to add or to ask, see you there!

If you haven't stopped reading, you're one of the few that still prefer the old school README . Nice!

Below you'll find a curated list of bioinformatics training material. All material is:

In a GitHub or GitLab repository (repositories in self-managed instances of GitLab are not supported anymore..)
Free to use
Written in markdown or similar

NOTE: This list of courses is selected only based on the above criteria. There are no checks on quality.

Contents

Scripting and languages
- Version control
- Unix/Linux
- Python
- R
- Quarto
- Shiny
- Julia
- Data visualization
- Java
- GNU Make
- MATLAB/Octave
- SQL
- C/C++
- Rust
Computational methods and pipelines
Omics analysis
Reproducibility and data management
Statistics and machine learning
Others
- General

Scripting and languages

Version control

Unix/Linux

Python

R

Quarto

Shiny

Julia

Data visualization

Java

BioJava biojava/biojava-tutorial | website

GNU Make

MATLAB/Octave

Software Carpentry swcarpentry/matlab-novice-inflammation | website

SQL

C/C++

LiaBooks ... by LiaScript LiaBooks/C-Programming | website

Rust

Google google/comprehensive-rust | website

Computational methods and pipelines

Containerization

Galaxy

High performance computing

Workflows

Image analysis

Cloud computing

Omics analysis

Genomics

Next generation sequencing

Transcriptomics

RNA-seq

Single-cell sequencing

Variant analysis

ChIP-seq

Comparative genomics

Epigenetics

Genome annotation

Katharina Hoff KatharinaHoff/BRAKER-TSEBRA-Workshop

Genome assembly

UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2020-Genome_Assembly_Workshop

Metagenomics

Epidemiology

Microbiology

bioinformatics.ca bioinformaticsdotca/BMB_2024

Multiomics

Spatial transcriptomics

Long read sequencing

Metabolomics

bioinformatics.ca bioinformaticsdotca/MET_2023

Proteomics

Pathways and Networks

Reproducibility and data management

Data management

FAIR data

Reproducibility

Statistics and machine learning

Data science

Statistics

Machine learning

Others

General

training-collection's People

Contributors

Stargazers

Watchers

Forkers

wandrilled sateeshperi sbwiecko biocoderr estellad michael-olufemi winfrednyoroka gray-tu boston123456 hrhotz 208sp ccwu1212 alavrinienko svpipaliya sunnyev cigdemozen amystonelake ravindra-raut mahendra687 dawit-asnake robertoalvarezm nirmal2310 rlebron-bioinfo ymolinac kikegoni madmolecularman nxgendev-kyle nxgenmdx marencc ronfinn marconotaro das2000sidd anu-bioinfo genostack dereckmezquita biosharp-dotnet-labs margosolo johnyijaq sachinkavindaa aarthi31 animesh singlecoated dexwel mghanbari altingia blosberg odetteg kmdubi guo-cheng nickspizza001 matteobolner hasibaasma enricocid scienception jsgro pmb59 parisaabedi sajesan aptejada abedkurdi ilyaszarif ahkamsaddam cookiess im-sanka sebepedroslab peculiar97 ardeat mohmedsoudy genomicsnx kunalgroy isabel-thompson xiaohan2013 leandroamoras kinene1 bio-mingchen bishnukuet training-resources chris-kreitzer wilsonjsjunior sridhar0605 sandyyy123 romaro-gomes scriptsman tenglongli marynjerey coolboy-up xrcham avivleemann benjamcm tony2015116 oschwengers salimdason rnaimehaom lindalynne koushik20 dktanwar monicambabazi ming-lian sadafraza zhenyanluo

training-collection's Issues

add advanced stats course

https://sib-swiss.github.io/advanced-statistics/

add materials related to R/python

https://github.com/bradleyboehmke/Intro-to-R-Bootcamp
http://uc-r.github.io/r_bootcamp

https://www.tidytextmining.com/
https://github.com/dgrtwo/tidy-text-mining

https://jakevdp.github.io/PythonDataScienceHandbook/
https://github.com/jakevdp/PythonDataScienceHandbook

https://jakevdp.github.io/WhirlwindTourOfPython/index.html
https://github.com/jakevdp/WhirlwindTourOfPython

https://github.com/rstudio/rmarkdown-book
https://bookdown.org/yihui/rmarkdown/

https://jennybc.github.io/purrr-tutorial/index.html
https://github.com/jennybc/purrr-tutorial

https://github.com/jennybc/happy-git-with-r
https://happygitwithr.com/

Other lists:
https://github.com/bradleyboehmke/data-science-learning-resources
https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources

Add Andy's brain book

https://github.com/andrewjahn/AndysBrainBook/blob/master/docs/index.rst

add efficient r programming book

https://csgillespie.github.io/efficientR/

Add intro to ds box courses

https://datasciencebox.org/
https://www.introdata.science/
https://introds-2020.netlify.app/

Add biodata science material Love

https://biodatascience.github.io/compbio/

Add material of bioinformatics.ca

https://bioinformaticsdotca.github.io/

Add awesome-workshop courses

https://github.com/awesome-workshop

add material of cfde

https://github.com/nih-cfde/training-and-engagement/wiki/
https://ngs-docs.github.io/2021-august-remote-computing/

Add bioschemas markup for ingestion to TeSS

It would be great if the html version were enhanced with bioschemas annotation so content can be automatically indexed via TeSS:

"Structured Data Types"
https://tess.elixir-europe.org/about/registering#:~:text=Structured%20Data%20Types

Setup CI

Set up CI workflows for style/link checking, e.g.:

Add mcelreaths stats course

https://github.com/rmcelreath/stat_rethinking_2022

add datascience book

https://github.com/rafalab/dsbook

Add fastai course

https://github.com/fastai/course20
https://book.fast.ai/

Add material of Ted Laderas

https://github.com/laderast/bash_for_bioinformatics
https://github.com/laderast/RBootcamp
https://github.com/laderast/gradual_shiny

Add RNA-seq material of EBI

https://www.ebi.ac.uk/training/materials/bioinformatics-immunologists-materials/rna-sequencing/single-cell-rna-seq-analysis/
https://mperalc.gitlab.io/scRNA-seq_workshop_2021/
https://mperalc.gitlab.io/bulk_RNA-seq_workshop_2021/

Dynamic badges

Initiate a dynamic badge to count the number of courses in the repo:
https://schneegans.github.io/tutorials/2022/04/18/badges

Add: Nextflow Course

https://training.seqera.io/

Add belgian RDM guide

https://github.com/ELIXIR-Belgium/rdm-guide

Add this course

https://github.com/hemberg-lab/scRNA.seq.course

add diy transcriptomics

https://github.com/DIYtranscriptomics/DIYtranscriptomics.github.io
https://diytranscriptomics.com/

Add CRG courses

https://biocorecrg.github.io/courses

Add NF core course

https://biocorecrg.github.io/CoursesCRG_Containers_Nextflow_May_2022/nf-core.html

Add CWL course of BioDataAnalysisGroup

Can be found here: https://github.com/BiodataAnalysisGroup/intro-to-cwl-docker

add single cell course to list

https://nbisweden.github.io/excelerate-scRNAseq/session-celltypeid/celltypeid.html

Add gh material written here

https://amandamiotto.github.io/HackyHourBookmarks/
Make sure to ref

Add learngemocis.dev

https://github.com/stjude/learngenomics.dev

maybe interesting material to add

How to annotate some sequence by sequence conservation across the same family of proteins?

Add rmd workshop

https://github.com/jthomasmock/rmd-nhs/tree/master/workshop

SPARQL-Training: how to include?

How can we include https://github.com/sib-swiss/sparql-training? in the list?

add moderndrive for R

https://github.com/moderndive/ModernDive_book

add material Sean Davis

https://seandavi.github.io/ITR/RangesAndSignal.html

SPHN Training material

Hi Geert. Here is the current list of SPHN Training material:

prediction of secondary structure from protein sequence

another task that people might like to know about

add online R learning by Chenxin Li

https://github.com/cxli233/Online_R_learning

Add FAIR cookbook page

Can be found here: https://fairplus.github.io/the-fair-cookbook/content/home.html

courses DMP

https://github.com/korbinib/DMP-writing-workshop

https://github.com/elixir-oslo/fair-dm-lifesci-june-2022

add nf core variant calling to list

https://sateeshperi.github.io/nextflow_varcal/nextflow/

Count courses badge pipeline failes

Updated PAT, but error persists:

Failed to create gist, response status code: 401, status message: Unauthorized

add carpentries data wrangling course

https://datacarpentry.org/wrangling-genomics/

Add dataviz book

https://github.com/JoachimGoedhart/DataViz-protocols

Add Melbourne bioinformatics docs

https://github.com/melbournebioinformatics/MelBioInf_docs

Add R/bioconductor course biocommons

https://saskiafreytag.github.io/biocommons-r-intro/

Add rstudioconf workshops

E.g.: https://rstudio-conf-2022.github.io/ggplot2-graphic-design/

Add edinburgh carpentries material

https://github.com/edcarp

Add plants and python

https://plantsandpython.github.io/PlantsAndPython/00_Opening_page.html

Add SIB course

https://github.com/sib-swiss/Introduction-to-statistics-with-R

Add introds.org

https://www.introds.org/

Add material fasteR

https://github.com/matloff/fasteR

Bioc course carpentries

https://carpentries-incubator.github.io/bioc-project/

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