jlchen5/CT-analysis

Performing the Circuit topology method in cancer genome

CT analysis

• Circuit Topology approach in Cancer Research and Immune cells

• TCGA data of RNA-seq, WGS, scRNA-seq and Hi-C, scHi-c, etc.

• In this repo, based on the single-cell Hi-C data.

Steps

• We extract the circuit topology matrix by Extract_CT_scHiC.ipynb or use Extract_topology.ipynb from .pdb files, and combined the gene abundance with bin_RNAseq.ipynb and CoupleRNAseq_CT.ipynb scripts alsa gene annotation and gene expression data (recommend the raw counts).

• We analyze the single-cell RNA-seq data by scRNAseq_analysis.ipynb, which can combine the multiple data set annotate the cell types. Then we use the scRNA_TF_acti_infer.ipynb to infer the transcription factors activity and scRNAseq_pthway_infer.ipynb to deduce pathway activity.

• We analyze the single cell persudotime via the scRNA-seq data.

• The scRNA-seq data was analyzed with scHi-C data.

• We seperate the hic contact files to 2 files which _1.bed and _2.bed.The motif analysis is performed by run_homer.sh.

  bash run_homer.sh

• We use CTforCumulativeAnalysis to generate the csv files and as Cumulative_analysis.ipynb input files.

• This script: Extract_topology is for extracting the topology information from pdb files and we can get more data because the pdb files have larger size.

More details

If your wanna know more information about this project and progress, please see Procedure_Circuit_Topology.md

License

This package is free software; you can redistribute it and/or modify it under the terms of the MIT License as published by the Free Software Foundation; either version 2 of the License or (at your option) any later version.