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Load_Normalize_Example - loads 100kb chr8 Hi-C data from a text file. Then removes unmappable regions (repetative regions like centromeres), normalizes the data using three different methods and plots the raw and normalized matrices. The normalization methods are:
  1. Spectral Identification of Topological Domains by Chen et al, Bioinformatics May 2016
  2. Nucleome analysis of a colorectal cancer cell line reveals structure-function relationships by Seaman et al, Mol Canc Res March 2017
  3. Iterative Correction of Hi-C Data Reveals Hallmarks of Chromosome Organization by Imakaev et al, Nat Methods Oct 2012

TAD_methods - performs 3 methods of TAD calculation and plotting on a 100kb resolution chromsome 22 Hi-C matrix from fibroblasts. Normalization methods are:
  1. Spectral Identification of Topological Domains by Chen et al, 2016
  2. Multiscale Identification of Topological Domain in Chromatin by Filippova et al, 2013
  3. Topological domains in mammalian genomes identified by analysis of chromatin interactions by Dixon et al 2012
  note: warnings "Matrix is singular to working precision." during TAD_HMM is normal.

TranslocationAnalysis_100kb - Analyzes t(6;14) in 100 kb resolution data including identifying the site of translocation, and constructing the translocated chromosome. It also includesnormalizing Chr 6, 14, and t(6;14), and calculating TADs. Demonstrates plotting abilities including plotting Hi-C, RNA-seq, Fiedler vector, and TADs in one figure.

TranslocationAnalysis_read -  Loads read level data from output text files produced by Homer and other software. Uses read level data for HT-29 from chromosmes 6 and 14 to identify the site of translocation at high resolution.

PhasePortrait - demonstrates loading RNA-seq data and converting raw data into binned data. Plots time series data in three dimensions with the x-y dimension showing Hi-C matrices and the z-direction showing time. Also calculate necessary data and and a phase plane which shows how structure, as measured by the Fiedler number and function as measured by the square root of the average FPKM for all genes in the chromosome (or region) for chromosome 22 and a single TAD in the chromsome for the fibroblast time series.

HT29_2D_12hr_100kb_chr8.txt - text file including 100 kb resolution chromosome 8 from a 12 hour time point of 2D grown HT-29 cells, originally published in Nucleome analysis of a colorectal cancer cell line reveals structure-function relationships by Seaman et al, Mol Canc Res March 2017 chr22_100kb_HiC_FibTS.mat - 100 kb resolution chr 22 RNA_seq and Hi-C matrix of all time points from Functional organization of the human 4D Nucleome by Chen et al 2015.
chr6_chr14_reads_HT29.mat - chr 6, 14 and 6-14 inter-chr read locations from the 2D 12 hr sample  published in Nucleome analysis of a colorectal cancer cell line reveals structure-function relationships by Seaman et al, Mol Canc Res March 2017.
readData_optional/ FibTs0_chr6_interReads.txt & FibTs0_chr12_interReads.txt - text files that contain the read pairs for all inter-chromosomal reads for chromsomes 6 and 14 respectively. Published in Nucleome analysis of a colorectal cancer cell line reveals structure-function relationships by Seaman et al, Mol Canc Res March 2017.
chr6_chr14_100kb_RNA_HT29.mat - chr 6 and 14 RNA-seq binned into 100 kb bins to match the Hi-C data published in Nucleome analysis of a colorectal cancer cell line reveals structure-function relationships by Seaman et al, Mol Canc Res March 2017.
chr6_chr14_100kb_HT29.mat - chr 6, 14 and 6-14 inter-chr matrix from the 2D 12 hr sample at 100kb resolution published in Nucleome analysis of a colorectal cancer cell line reveals structure-function relationships by Seaman et al, Mol Canc Res March 2017.
fib_ts_RNA_rawCounts.csv - all raw count gene expression estimates for all time points in the cell cycle synchronized proliferating  fibroblasts. Originally published in Functional organization of the human 4D Nucleome by Chen et al 2015
GenInfo_loc.mat - gene names, brief descriptions, and locations for hg19 reference genome. Also includes the length of each chromosome in 100 kb bins.

BlockToepNorm - performs copy number based normalization
cbar - adds small colorbars to at the top right. Sized based on number of subplots
Draw_TADs - plots Hi-C data with TAD boundaries overlaid
FindGenBin - looks up a gene's location.
FindGenLocation - Calculates which bin(s) a gene is locatated in.
HiC_load_cool - loads Hi-C matrices from .cool files, HDF5 binary sparse matrix format
HiC_load_mat - loads n x n Hi-C matrices from text files (including homer format)
HiC_plot - plots Hi-C matrix in log2 scale
HiC_remove_cent - removes centromeres from Hi-C matrices
HicRna_plot - plots HiC, RNA-seq, TADs, and Fiedler vector in various combinations
HicTensorFig - plots time series data in 3D. z-dimension indicates time while each x-y plane shows the Hi-C and RNA-seq for a single time point.
ICE - performs iterative correction and eigenvector decomposition normalization
Load_TSV - loads tab seperated value files containing read pairs of Hi-C data.
Mat2Val - calculate Fiedler number, Fiedler vector, Von Neumann Entropy, and more from matrices depending on provided type.
PltFV - plots Fiedler vector bar graph with positive and negative values colored seperately
PltPhasePlane - plots a phase protrait/plane showing a projection of structure and function over time.
RNA2Bin - converts gene resolution RNA-seq data into bin resolution.
saveHiC - prints a Hi-C matrix to a csv (text) file.
saveTADs - prints vector of TAD bounds to a csv (text) file.
TAD_DP1 - performs dynamic programming / multiscale TAD analysis
TAD_HMM - performs Hiden Markov Model based algorithm for TAD analysis.
TAD_Laplace - performs iterative, Fiedler number based TAD analysis
ToepNorm - performs Toeplitz based normalization
TranslocHiC - constructs translocated chromsomes matrices from parts