Issues

• Summarize FCC scores across CRE clusters and visualize

  ReddyLab/Proj_ENCODE_FCC#44 · Filter by author clintko opened on Jun 13, 2025

• Summarize the enriched TFs for each cluster into a table

  ReddyLab/Proj_ENCODE_FCC#43 · Filter by author clintko opened on Jun 13, 2025

• Apply the updated enrichment test for each CRE cluster across all ChIP-seq factors

  ReddyLab/Proj_ENCODE_FCC#42 · Filter by author clintko opened on Jun 13, 2025

• Performed Phenograph clustering on CRE regions by their ChIP-seq log2 fold changes to identify CRE clusters

  ReddyLab/Proj_ENCODE_FCC#41 · Filter by author clintko opened on Jun 13, 2025

• Visualize ChIP-seq scores on the UMAP for some histone marks and TFs

  ReddyLab/Proj_ENCODE_FCC#40 · Filter by author clintko opened on Jun 13, 2025

• Label cCREs annotation on the UMAP

  ReddyLab/Proj_ENCODE_FCC#39 · Filter by author clintko opened on Jun 13, 2025

• Label proximal/distal CREs on the UMAP

  ReddyLab/Proj_ENCODE_FCC#38 · Filter by author clintko opened on Jun 13, 2025

• Performed UMAP on finalized CREs and visualize the two-dimentional embedded of the regions

  ReddyLab/Proj_ENCODE_FCC#37 · Filter by author clintko opened on Jun 13, 2025

• Annotate ATAC with FCC peaks: summarize and visualize summary of the union table

  ReddyLab/Proj_ENCODE_FCC#36 · Filter by author clintko opened on Jun 11, 2025

• Annotate ATAC with FCC peaks: summarize and visualize the STARR/MPRA/CRISPR CRE table

  ReddyLab/Proj_ENCODE_FCC#35 · Filter by author clintko opened on Jun 11, 2025

• Annotate ATAC with FCC peaks: finalize CRE table for UMAP/cluster analysis

  ReddyLab/Proj_ENCODE_FCC#34 · Filter by author clintko opened on Jun 11, 2025

• Annotate ATAC with FCC peaks: generate union peak table as resource

  ReddyLab/Proj_ENCODE_FCC#32 · Filter by author clintko opened on Jun 11, 2025

• Annotate ATAC with FCC peaks: summarize and visualize proximal/distal-active/repressive CRE table

  ReddyLab/Proj_ENCODE_FCC#30 · Filter by author clintko opened on Jun 11, 2025

• Visualize ChIP-seq heatmap across CREs (proximal/distal-active/repressive) vs inactive regions

  ReddyLab/Proj_ENCODE_FCC#27 · Filter by author clintko opened on Jun 10, 2025

• Annotate ATAC with FCC peaks and arrange the intersected region pairs

  ReddyLab/Proj_ENCODE_FCC#20 · Filter by author clintko opened on Jun 9, 2025

• Section 02 | Region Summary

  ReddyLab/Proj_ENCODE_FCC#12 · Filter by author clintko opened on Jun 6, 2025

• Section 04 | Analysis | UMAP/Cluster analysis of CREs

  ReddyLab/Proj_ENCODE_FCC#10 · Filter by author clintko opened on Jun 5, 2025

• Section 03 | Analysis | Characterization proximal/distal CREs by ChIP-seq coverage

  ReddyLab/Proj_ENCODE_FCC#9 · Filter by author clintko opened on Jun 5, 2025

• Section 02 | Region Annotation

  ReddyLab/Proj_ENCODE_FCC#8 · Filter by author clintko opened on Jun 5, 2025

• Section 02 | Region Coverage | ChIP-seq

  ReddyLab/Proj_ENCODE_FCC#7 · Filter by author clintko opened on Jun 5, 2025

• Section 02 | Region Coverage | FCC

  ReddyLab/Proj_ENCODE_FCC#6 · Filter by author clintko opened on Jun 5, 2025

• Section 01 | Prepare Data | Region/Peak calls and annotations

  ReddyLab/Proj_ENCODE_FCC#5 · Filter by author clintko opened on Jun 5, 2025

• Section 01 | Prepare Data | ChIP-seq

  ReddyLab/Proj_ENCODE_FCC#4 · Filter by author clintko opened on Jun 5, 2025

• Section 01 | Prepare Data | HiC

  ReddyLab/Proj_ENCODE_FCC#3 · Filter by author clintko opened on Jun 5, 2025

• Section 01 | Prepare Data | FCC

  ReddyLab/Proj_ENCODE_FCC#2 · Filter by author clintko opened on Jun 5, 2025