# Reference github folder: https://github.com/bborsari/Borsari_et_al_transdifferentiation_chromatin

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# March 1st, 2021
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# Perform the following tasks for each tissue (heart & midbrain)

# 1. subset the matrix to keep:
# - silent genes (aka genes with 0 TPMs in all time-points)
# - expressed genes (aka genes with at least 5 TPMs in at least one time-point (both replicates))

# 2. convert the matrix to log2 (TPM +1)

# 3. apply quantile normalization across replicates and time-points 
# using the preprocessCore library
# (see script: quantile.normalization.R)

# 4. get the average matrix of rep 1 and rep 2 matrices after quantile normalization

# 5. run maSigPro to obtain genes that are differentially expressed during the time-course
# (see script: maSigPro.wrapper.R)

# as a guideline, follow:
# - commands 3-5 in Borsari_et_al_transdifferentiation_chromatin/analysis/all.marks/expression/cmnd.txt 
# - commands 1-4,6 in  Borsari_et_al_transdifferentiation_chromatin/analysis/all.marks/expression/QN.merged/cmnd.txt