Useful Links for Bulk RNA-seq

1. • RNAseq training by  Harvard Chan Bioinformatics Core (HBC)  -  https://hbctraining.github.io/Training-modules/planning_successful_rnaseq/

   • https://courses.ucsf.edu/course/view.php?id=6137

   • https://github.com/zhxiaokang/RASflow/blob/master/Tutorial.pdf

   • https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

   • complete step-by-step with scripts - https://bitbucket.org/adinasarapu/ibs_class/src/master/

• Snakemake workflow - https://github.com/zhxiaokang/RASflow/blob/master/Tutorial.pdf

• RNA-seq workflow: gene-level exploratory analysis and differential expression - https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

• Nanopore data analysis(NB: site hosts several protocols) - https://www.protocols.io/view/nanopore-data-analysis-14egn8xqpg5d/v2

• https://www.hadriengourle.com/tutorials/

• RNAseq end-to-end analysis in R (RSubread) - https://www.alzheimersworkbench.ucsd.edu/EndToEndAnalysis_RNASeq.html

• RNAseq end-to-end analysis (Good bash commands) 

github.com/grimmlab/BookChapter-RNA-Seq-Analyses 

Useful links for scRNA-seq 

• scRNAseq -  https://carmonalab.github.io/ProjecTILs_CaseStudies/Bassez_BC.html

• scRNAseq - https://satijalab.org/seurat/articles/pbmc3k_tutorial.html

• scRNAseq - https://carmonalab.github.io/ProjecTILs.demo/tutorial.html

• scRNAseq - https://carmonalab.github.io/ProjecTILs_CaseStudies/Sandu_LCMV.htm

Differentially Expressed Genes Network Analysis (Using Cytoscape)

• Workflow for a set of DEG - https://cytoscape.org/cytoscape-tutorials/protocols/differentially-expressed-genes/#/

• RNA-seq Data Network Analysis ( with Cytoscape) - https://cytoscape.org/cytoscape-tutorials/protocols/rna-seq-data-analysis/#/

• Phyloseq - https://joey711.github.io/phyloseq/index.html

• PICRUST2 - https://github.com/picrust/picrust2/wiki/PICRUSt2-Tutorial-(v2.4.2)#tutorial-dataset

• https://github.com/tanyabrown9/Resilient_vs_Susceptible_Mcapitata

EMBL TRAININGS - http://ftp.ebi.ac.uk/pub/training/2021/

https://maayanlab.cloud/biojupies/help biojupies

Very good book on the underlying algorithms  for most bioinformatics tasks.  http://readiab.org/introduction.html