AtacAnnoR is a novel scATAC-seq cell type annotation method using scRNA-seq data as the reference.
AtacAnnoR performs two rounds of annotation, which annotate scATAC-seq cells at gene-level and genome-wide-level, respectively.
In the first round gene-level annotation, AtacAnnoR compares gene activity profiles derived from scATAC-seq data with reference gene expression profiles, assigning a subset of query cells with reference cell type labels.
In the second round genome-wide-level annotation, AtacAnnoR predicts the labels of the remaining query cells using a meta-program matrix derived from genome-wide ATAC-peaks.
For more details about AtacAnnoR, please refer to our publication: https://doi.org/10.1093/bib/bbad268
if (!requireNamespace("devtools", quietly = T)) install.packages("devtools")
devtools::install_github("zdebruine/RcppML") # v0.5.4 or higher
devtools::install_github("TianLab-Bioinfo/AtacAnnoR",force = T)
library(AtacAnnoR)
pred <- RunAtacAnnoR(ref_mtx = SeuratObj_RNA[['RNA']]@counts,
ref_celltype = SeuratObj_RNA$true,
query_gene_activity = SeuratObj_ATAC[['ACTIVITY']]@counts,
query_peak_counts = SeuratObj_ATAC[['ATAC']]@counts)
SeuratObj_ATAC <- RunAtacAnnoR_Signac(query_SeuratObj = SeuratObj_ATAC,
query_ga_assay = 'ACTIVITY',
query_peak_assay = 'ATAC',
ref_SeuratObj = SeuratObj_RNA,
ref_assay = 'RNA',
ref_ident = 'true')
The predicted labels can be accessed using SeuratObj_ATAC$final_pred
.
query_ArchRproj <- RunAtacAnnoR_ArchR(query_ArchRproj = query_ArchRproj,
ref_mtx = SeuratObj_RNA[['RNA']]@counts,
ref_celltype = SeuratObj_RNA$true)
The predicted labels can be accessed using query_ArchRproj$final_pred
.
query_snapObj <- RunAtacAnnoR_SnapATAC(query_snapObj = query_snapObj,
ref_mtx = SeuratObj_RNA[['RNA']]@counts,
ref_celltype = SeuratObj_RNA$true)
The predicted labels can be accessed using query_snapObj@metaData$final_pred
.
query_cds <- RunAtacAnnoR_Cicero(query_cds = query_cds,
query_gene_activity = query_gene_activity,
ref_mtx = SeuratObj_RNA[['RNA']]@counts,
ref_celltype = SeuratObj_RNA$true)
The predicted labels can be accessed using query_cds@colData$final_pred
.
Lejin Tian: ljtian20@fudan.edu.cn