MIMB

Chapter submission for MIMB Summer 2021

Outline:

Brief literature review
Data formats -- what is required, depending on availability
- Chr start stop
- Cg annotation (illumina)
- Other → some method for relating genome location to binding
Pipeline: 0. FIMO scan & open-access data
1. (py)bedtools
2. integrating
3. Integrating into netzoo bipartite
4. Integrating into other GRN framework 1. Smaller GRN models (TF-gene subsets) could just merge with methyl-motif and reduce their estimates where overlap / downweight (GRN estimate x 1- avg meth ratio)
5. Benchmarking against ChIP-seq

Name		Name	Last commit message	Last commit date
Latest commit History 16 Commits
bench		bench
.DS_Store		.DS_Store
.gitignore		.gitignore
B.txt		B.txt
Building_a_methylation-informed_GRN.ipynb		Building_a_methylation-informed_GRN.ipynb
Building_a_methylation-informed_GRN_rxiv.ipynb		Building_a_methylation-informed_GRN_rxiv.ipynb
LTRC_DM_ipf_blood.R		LTRC_DM_ipf_blood.R
M5568_1.02.txt		M5568_1.02.txt
Motif_BS_Chmax_refseq.txt		Motif_BS_Chmax_refseq.txt
PRS_MMoll.ipynb		PRS_MMoll.ipynb
README.md		README.md
Untitled.ipynb		Untitled.ipynb
anova.png		anova.png
corr_LTRC.py		corr_LTRC.py
generic_motif.txt		generic_motif.txt
generic_motif_250.txt		generic_motif_250.txt
hg38_Tss_coordinates.csv.zip		hg38_Tss_coordinates.csv.zip
hg38_gene_coord.txt		hg38_gene_coord.txt
hg38_refseq_201811.txt		hg38_refseq_201811.txt
human.hg38.genome		human.hg38.genome
log_anova.png		log_anova.png
maxHits.py		maxHits.py
ppi2015_freezeCellLine.txt		ppi2015_freezeCellLine.txt
slop_mega.sh		slop_mega.sh
take_uniq.py		take_uniq.py