inst/rstudio/templates/common/README.md

In lpantano/bioprojectR: Template for Rstudio project for Bioinformatics

PROJECT_NAME

Summary

Methods

Standard methods are explained inside the report at the end.

Publication policy

"The authors would like to thank Lorena Pantano of the PILM Bioinformatics Core, Picower Institute of Learning and Memory, Cambridge, MA for assistance with RNAseq analysis."

https://github.mit.edu/pages/PILM-bioinformatics/knowledgebase/admin/projects/

Data

Temporarly in OpenMind /om/user/lpantano/projects/PROJECT_NAME

Results

Shared dropbox: https://www.dropbox.com/home/DROPBOX_PATH/PI/PROJECT_NAME

Inside reports folders:

• MultiQC: Qc metrics for the analysis and all samples.
• YY: differential expression (DE) analysis for YY genotype
• de.html: DE report
• de/results/counts: expression at different normalization levels
• de/results/differential_expression/comparison: DE results
• ZZ: differential expression analysis for mut genotype (same folder structure)
• meta_de_results.csv.gz: all genes results from DE analysis

Resources

Functional analysis: Look at the tip of the week in this newsletter to know the options: https://github.mit.edu/pages/PILM-bioinformatics/secure-newsletters/2019/05/pilm-bioinformatics-newsletter-week-20-functional-analysis-do-it-right/

lpantano/bioprojectR documentation built on July 16, 2019, 4:30 a.m.