DeCEP

A novel method for deciphering context-specific gene programs using single-cell and spatial transcriptomics data

DeCEP is a computational framework designed to characterize context-specific gene programs using scRNA-seq and ST data. DeCEP leverages functional gene lists and directed graphs to construct functional networks underlying distinct cellular or spatial contexts. It then identifies context-dependent hub genes based on the network topology and assigns gene program activity to individual cells or spatial locations.

Installation

You can install the released version of DeCEP with:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("Lin-bioinfo/DeCEP")

Getting started

1. Static cellular contexts (the test data can be downloaded from this drive_link.

library(DeCEP)
library(parallel)
cores = detectCores(logical = FALSE) - 1

load("DeCEP_data_sc_discrete.RData")
dat = pre_sc(x = x, label = label, modes = c("discrete"), genelist = genelist, transition_point = NULL)

cl = makeCluster(cores)
net_A = net_sc(dat$A, modes = c("discrete"), genelist = genelist, select = 1, cluster = cl, seed = 1)
cl = makeCluster(cores)
net_B = net_sc(dat$B, modes = c("discrete"), genelist = genelist, select = 1, cluster = cl, seed = 1)

DeCEP_score_A = ident_sc_score(dat$A, net_A, seed = 1)
DeCEP_score_B = ident_sc_score(dat$B, net_B, seed = 1)
DeCEP_state_A = ident_sc_state(DeCEP_score_A)
DeCEP_state_B = ident_sc_state(DeCEP_score_B)

2. Dynamic cellular contexts

library(DeCEP)
library(parallel)
cores = detectCores(logical = FALSE) - 1

load("DeCEP_data_sc_continuous.RData")
dat = pre_sc(x = x, label = label, modes = c("continuous"), genelist = genelist, transition_point = 20)

cl = makeCluster(cores)
net = net_sc(dat, modes = c("continuous"), genelist = genelist, select = 1, cluster = cl, seed = 1)

DeCEP_score = ident_sc_score(x, net, seed = 1)
DeCEP_state = ident_sc_state(DeCEP_score)

3. Spatial contexts

load("DeCEP_data_st.RData")
st_anno = pre_st(x_counts, coords, genelist, ref, cell_state, core_number = 2)
roiID = st_anno[st_anno$DeCEP_state == "High", "spot_ID"]
x_st = net_st_pre(x_data, coords, genelist, roiID, r = 60)

cl = makeCluster(cores)
net_st = net_st(x_st$dat, genelist, select = 1, cluster = cl, seed = 1)
involvedID = c(roiID, x_st$neighborID)
DeCEP_score = ident_st_score(x_impute, involvedID, net_st)   # use data after imputation

License

DeCEP is licensed under the GNU General Public License v3.0.

Citation

Please cite the following article if you use DeCEP in your research:

Contact

Should you have any questions, please feel free to write issues for this repository or contact the author directly at [email protected].