Repository for scChIX
2021-05-01
This is the R package for deconvolving multiplexed histone modifications (https://www.biorxiv.org/content/10.1101/2021.04.26.440629v1).
2023-01-01
More has now been added for the journal version of the paper: "scChIX-seq infers dynamic relationships between histone modifications in single cells" https://www.nature.com/articles/s41587-022-01560-3.
Specifically we've added in the vignettes:
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simulation study to show how scChIX-seq performs on ground truth data. Simulation studies and downstream analysis of estimates versus ground truth:
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application of scChIX-seq on early organogenesis, seeing relationships between heterochromatin and active transcription. Comparing cell type and heterochromatin relationships, and global changes in ratios of two histone modifications:
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Uncover dynamic relationships between histone modifications by inferring two pseudotime labels during differentiation. Inferring dual continuous pseudotime during macrophage differentiation
library(devtools)
devtools::install_github("jakeyeung/scChIX")
Follow the vignettes for an example of deconvolving the multiplexed signal. The output is a linked UMAP. In the example it is H3K27me3 UMAP on the left, H3K9me3 UMAP on the right, with lines connecting the two maps together:
Here are a list of vignettes for guided analysis:
Simulation studies and downstream analysis of estimates versus ground truth:
Analysis of scChIX downstream:
Inferring dual continuous pseudotime during macrophage differentiation