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
- data analysis
- single cell
- transcription factor
- circulating tumor
- genome wide
- rna seq
- gene expression
- cell free
- dna damage
- single molecule
- dna methylation
- electronic health record
- induced apoptosis
- big data
- high resolution
- nucleic acid
- randomized controlled trial
- oxidative stress
- cell cycle arrest
- signaling pathway
- systematic review
- cell therapy
- machine learning
- circulating tumor cells
- bone marrow
- deep learning
- crystal structure
- cell proliferation
- artificial intelligence
- genome wide association study
- loop mediated isothermal amplification
- real time pcr
- photodynamic therapy