The source code for the analysis of snRNA-seq and scATAC-seq of amphioxus.
The package for building the developmental tree can be found at: https://github.com/XingyanLiu/stagewiseNN
Citation:
Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al., Joint profiling of gene expression and chromatin accessibility of amphioxus development at single-cell resolution, Cell Reports (2022), https://doi.org/10.1016/j.celrep.2022.110979
| File | Description |
|---|---|
| rna_proc_stagewise.py | preprocessing, clustering, and visualization of the snRNA-seq data |
| de-nearstage.R | differential expression analysis - current vs the previous stage |
| atac_preproc.R | preprocessing and visualization of the scATAC-seq data |
| atac2ga_cicero.R | compute the gene activities (GA) from the scATAC-seq data |
| omics_integration-Harmony.R | integration of snRNA_seq and scATAC-seq data using Harmony, and KNN-based label transfer |
| omics_integration-Seurat.R | integration of snRNA_seq and scATAC-seq data using Seurat |
| lineage_dynamics-swnn-GA.ipynb | using StagewiseNN to integrately visualize the scATAC-seq data across six stages (based on GA) |
| GRN-scenic.py | compute the TF-target pairs using pySCENIC |
| GRN-intersection.py | compute the species-conserved TF-target pairs |
| GRN-filter.py | filter TF-target pairs based on their DE lineages |
| src/* | general utils functions (Python) |
| RFunx.R | general utils functions (R) |
| RFunxATAC.R | utils functions for analysis related to scATAC-seq data |
| RFunxTreePlot.R | utils functions for plotting the tree |
| amph_tree-struct.R | main code for plotting the tree structure |
| amph_tree-web.R | main code for visualizing the expressions on the developmental tree |
| COLOR_SETS.R | the color set |