Deposited Data for the TICHR Project

This test dataset contains only data from chr2 and chr12. It is for https://tichr.readthedocs.io/en/latest and https://github.com/wangjk321/TICHR. It includes the following folders: Compute Test data for the “Compute Rg and RgX” section. It contains a set of DNase, H3K27ac, and Hi-C data; a set of downstream Hi-C processing data used to adjust the computed results; a gene blacklist used for result refinement; as well as test gene and site datasets. The .hic file can be downloaded from: https://www.encodeproject.org/files/ENCFF621AIY/@@download/ENCFF621AIY.hic SiteToGene Test data for the “Characterizing enhancer-promoter interactions” section. It contains multiple Rg and RgX DataFrames, as well as a gold-standard enhancer–promoter (E-P) interaction file. DEG Test data for the “DEG prediction and attributing transcriptional changes” section. It includes Rg and RgX DataFrames for two test datasets, used respectively for single-factor analysis and multiple-factor analysis. Treatment Test data for the “Regulation–transcription concordance analysis” section. It includes multiple Rg and RgX DataFrames for various factors before and after siNIPBL treatment. Negative Test data for the “Identifying negative regulation for context-specific regulators” section. It includes two datasets containing Rg and RgX DataFrames before and after treatment, used for the single-sample analysis and multi-sample analysis components. Large Test data for the “Cross-sample analysis of large-scale and single-cell data” section. It contains a bulk multi-sample dataset and a single-cell multi-sample dataset. TimeSeries Test data for the “Revealing time-series transcriptional dynamics” section. It includes a single-gene time-series RgX dataset and Rg/RgX DataFrames covering all time points of a time-series experiment.