Chromatin spatial organization plays a crucial role in gene regulation. Recently developed and prospering multiplexed DNA FISH technologies enable direct visualization of chromatin conformation in the nucleus. However, incomplete data caused by limited detection efficiency can substantially complicate and impair downstream analysis. Here, we present SnapFISH-IMPUTE that imputes missing values in multiplexed DNA FISH data. Analysis on multiple published datasets shows that the proposed method preserves the distribution of pairwise distances between imaging loci, and the imputed chromatin conformations are indistinguishable from the observed conformations. Additionally, imputation greatly improves downstream analyses such as identifying enhancer-promoter loops and clustering cells into distinct cell types. SnapFISH-IMPUTE is freely available at https://github.com/hyuyu104/SnapFISH-IMPUTE .
Keyphrases
- data analysis
- single cell
- transcription factor
- circulating tumor
- genome wide
- gene expression
- rna seq
- cell free
- dna damage
- single molecule
- dna methylation
- induced apoptosis
- electronic health record
- big data
- high resolution
- stem cells
- nucleic acid
- cell cycle arrest
- mesenchymal stem cells
- oxidative stress
- cell therapy
- binding protein
- circulating tumor cells
- molecular dynamics simulations
- randomized controlled trial
- quantum dots
- endoplasmic reticulum stress
- loop mediated isothermal amplification
- label free
- bone marrow
- cell proliferation
- mass spectrometry
- genome wide association