Further Reading - dieterich-lab/hbigs_course_2022 GitHub Wiki

Further Reading

Here you can find web pages and research papers on your topic of interest:

Key points in batch effects

Leek, Jeffrey T., et al. "Tackling the widespread and critical impact of batch effects in high-throughput data." Nature Reviews Genetics 11.10 (2010): 733-739. https://doi.org/10.1038/nrg2825

This work highlights the need to measure and, potentily, correct potential batch effects in high-throughput experiments. A hands-on workflow is presented here: http://jtleek.com/genstats/inst/doc/02_13_batch-effects.html#adjusting-for-batch-effects-with-combat

Best practices for RNA-Seq design and analysis

Conesa, A., Madrigal, P., Tarazona, S. et al. A survey of best practices for RNA-seq data analysis. Genome Biol 17, 13 (2016). https://doi.org/10.1186/s13059-016-0881-8

This seminal review presents the concepts of all steps in RNA-Seq experiment, from a computational perspective.

Exploratory analysis and differential gene expression workflow from gene counts in R

This is a very detailed guide on differential gene expression analysis.

Love, Michael I., et al. "RNA-Seq workflow: gene-level exploratory analysis and differential expression." F1000Research 4 (2015). https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

Differential transcript expression analysis

Similar to the above, but for transcript expression analysis.

Love, Michael I., Charlotte Soneson, and Rob Patro. "Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification." F1000Research 7 (2018). https://bioconductor.org/packages/release/workflows/html/rnaseqDTU.html

On the usage of workflow managers

Wratten, Laura, Andreas Wilm, and Jonathan Göke. "Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers." Nature methods 18.10 (2021): 1161-1168. https://www.nature.com/articles/s41592-021-01254-9

Vizualization

Databases

  • Ensembl: an Encyclopedia for functional genetics integrated with a genome browser.
  • Uniprot: the primary resource for protein sequence and functional annotation.
  • The Huma Protein Atlas: a recent resource that details protein function to the tissue level.