filter other genes except protein-coding genes
CMap/LINCS-based Drug repositioning analysis
Key Pathways
compare HIV drug genes and pathways with nCoV's
data:
final: raw read counts
documents:
slides
src/
# mapping
./0.0.1_mapping_cmd.sh
# merge data and gene symbols
./0.1_preprocessing.R
# Differential Expression Analysis for three comparsion pairs
./1.0_DE.R
./1.0_DE_q0.001.R
# norm all samples for PCA/Heatmap only.
./1.1_norm3groups.R
# Pathway analysis
./2.0_KEGG.R
# cogena analysis
./2.1_cogena.R
./2.3_cmap_lincs.R
Zhou, Z., Ren, L., Zhang, L., Zhong, J., Xiao, Y., Jia, Z., Guo, L., Yang, J., Wang, C., Jiang, S. and Yang, D., 2020. Heightened innate immune responses in the respiratory tract of COVID-19 patients. Cell Host & Microbe. https://doi.org/10.1016/j.chom.2020.04.017
Created: Jan 28, 2020