ENCODE FCC Project
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Analysis
Data
Code
Results
Setup
13 Prepare: ChIP-seq
Setup
01 Working Environment
02 Working Directory
03 Reference Files
04 Data Files
11 Prepare: FCC
12 Prepare: Hi-C
13 Prepare: ChIP-seq
14 Prepare: Region
15 Prepare: Others
12 Results (FCC)
12 Results (FCC)
13 Results (HiC)
14 Results (Region)
Prepare
FCC Data
Hi-C Data
ChIP-seq TF/Histone
Chromatin States and TF Modules
Peak calling
Open chromatin regions
Other Annotations
Coverage of FCC
FCC coverage at ATAC/DHS regions
Whole genome comparison of FCC assays
Rank normalized FCC effect size
Comparisons of FCC across genome annotations
Coverage of ChIP-seq
Region Annotation
Intersect/Summarize genomic annotaions by accessible regions
Intersect/Summarize FCC peak calls by accessible regions
Proximal/Distal-Active/Repressive CREs
Full CREs from STARR/MPRA/CRISPR assays
FCC correlation
FCC comparison
FCC enrichment
FCC UMAP/Cluster
FCC vs HiC
Test Notebook
Test ipynb for documentation
Setup
13 Prepare: ChIP-seq
13 Prepare: ChIP-seq