The original data was downloaded from GTEx portal: https://gtexportal.org/home/datasets
The processed data is available at https://zenodo.org/record/5784626#.YcC7lr3MLxR.
The original count data was downloaded from: http://bowtie-bio.sourceforge.net/recount/pooled/modencodefly_pooledreps_count_table.txt
The original metadata was downloaded from: http://bowtie-bio.sourceforge.net/recount/pooled/modencodefly_pooled_phenodata.txt
The original count data was downloaded from GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45719
The original HuRI protein-protein interaction data was downloaded from: http://www.interactome-atlas.org/data/HuRI.tsv
The original regulatome data was curated using the code from: https://github.com/leekgroup/networks_correction/blob/master/shellscripts/get_true_positive.sh.
The curated data is available at https://zenodo.org/record/5784626#.YcC7lr3MLxR.
The transcription factor gene list was downloaded from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825693/bin/NIHMS772895-supplement-Table_S2.xlsx
cor_est: remove batch effect, calculate the correlation matrix using GTEx data and adjust the correlation matrix
signal_ridge: ridgeplot showing the distribution of correlations for genes across different expression levels of GTEx data
corplot: boxplot for the relationship of IQR of correlations and expression levels
slope_min_IQR: scatter plot showing the relationship between the IQR of correlation and the expression level of GTEx data
qqplot: Q-Q plot showing the distribution difference of correlations between different expression levels of GTEx data
scRNA: ridgeplot of scRNA-seq example data
exp_signal: visualize the weighted distribution of expressions of genes, with the weight decided by the number of estimated co-expression partners, where co-expression signals are decided by setting a threshold on the absolute correlation
graphical_lasso: visualize the expression bias on co-expression network constricted by graphical lasso
PPI: visualize the weighted distribution of expressions of genes, with the weight decided by the number of interacting proteins of the corresponding protein, according to PPI database
bias_regulatome: visualize the weighted distribution of expressions of genes, with the weight decided by the number of interacting proteins of the corresponding protein, according to regulatome database
TP_Partition: compare the true positive of co-expression estimation before and after applying SpQN, conditional on the gene expression level, where co-expression signals are decided by setting a threshold on the absolute correlation, and the gene pairs corresponding to the interacting protein pairs in PPI were used as ground truth
TF_TP: compare the TF-related true positive of co-expression estimation before and after applying SpQN, conditional on the gene expression level, where co-expression signals are decided by setting a threshold on the absolute correlation, and the gene pairs corresponding to the interacting protein pairs in PPI were used as ground truth
functions: functions used in the visualization, batch effect removal and correlation matrix adjustment
scatter_nsampple_IQR: scatter plot showing the change IQR of correlations with the change of the number of PCs removed from the data
TF: visualize the number of predicted co-expressions among TF-related edges
drosophila: explore the mean-correlation relationship of drosophola developmental RNA-seq data
VST: examine the mean-correlation relationship after applying VST on the expression data
combat: examine the mean-correlation relationship after applying combat on the expression data
pool_tissues: examine the mean-correlation relationship for the GTEx data concatinating the expression data of three tissues