C2C12 myodifferentiation RNA-seq study
Analysis and scripts used in making of the manuscript figures
Contacts
Alexander Predeus, 2016-2018, predeus at gmail dot com
Publications
This work has been reported at Frontiers of Cardiovascular Biology conference (Vienna, April 20-22nd, 2018).
A. Predeus; OA. Ivanova; NV. Khromova; AM. Kiselev; DE. Polev; NA. Smolina; AA. Kostareva; RI. Dmitrieva, Pathway analysis of RNA-sequencing of various stages of myodifferentiaion identifies conditions favoring type I and type II fibers, and highlights increased efficiency of combined differentiation.
Full manuscript is currently in preparation.
Funding
This work has been funded by the Russian Science Foundation, grant # 16-15-10178.
Contents
The repository contains processed data from the GSE108503 RNA-Seq dataset (14 samples, 7 conditions).
It also contains all the code used in the downstream analysis (differential expression, pathway analysis).
Functions
- deseq_de - runs DESeq2 using expression matrix and a pair of conditions
- mass_deseq - runs many comparisons (via deseq_de) using a provided contrasts file
- pca12 - makes a well-annotated PCA plot
- mass_fgsea_deseq - runs pre-ranked fGSEA on all outputs of DESeq2
- eliminatePathways2 - attempts to group together similar pathways among all significant results
Source the functions in mydiff_functions.R before running myodiff_paper_analysis.R.