SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data.
Hongyu YuDaiqing WuGuning ShenMing HuYun LiPublished in: bioRxiv : the preprint server for biology (2024)
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 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
- oxidative stress
- dna damage
- data analysis
- induced apoptosis
- single cell
- transcription factor
- circulating tumor
- genome wide
- rna seq
- gene expression
- cell free
- single molecule
- electronic health record
- dna methylation
- big data
- high resolution
- nucleic acid
- circulating tumor cells
- binding protein
- randomized controlled trial
- systematic review
- deep learning
- machine learning
- mass spectrometry
- artificial intelligence
- cell death
- cell proliferation
- molecular dynamics simulations
- crystal structure
- genome wide association study
- real time pcr
- sensitive detection