复制 mkdir-p~/project/hic/data/myelom cd~/project/hic/data/data/myelom wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334nnn/GSM2334834/suppl/GSM2334834_U266_HindIII_HiC_TAD_40kb.tar.gz wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334nnn/GSM2334834/suppl/GSM2334834_U266_HindIII...
while only using 1/16 of the original sequencing reads. We show that the models learned from one cell type can be applied to make predictions in other cell or tissue types. Our work not only provides a computational framework to enhance Hi-C data resolution but also reveals features underlyin...
常用的分析软件 Software tools for Hi-C data analysis Hi-C可视化 image.png 数据分析 序列过滤 过滤原理 数据矫正 为什么要做数据矫正? Eitan Yaffe & Amos Tanay;2011 数据矫正效果 可做的分析 1.cis/trans互作比例 2.互作频率与距离有关 3.compartment分析 4.TAD分析 5.显著互作分析 image.png Hi-C的应...
Hi-C data is important for studying chromatin three-dimensional structure. However, the resolution of most existing Hi-C data is generally coarse due to sequencing cost. Therefore, it will be helpful if we can predict high-resolution Hi-C data from low-coverage sequencing data. Here we develop...
数据可视化,是关于数据视觉表现形式的科学技术研究。其中,这种数据的视觉表现形式被定为, 一种以某种 概要形式抽提出来的信息,包括相应信息单位的各种属性和变量。 Anything that converts data into a visual representation(like charts, graphs, maps,sometimes even just tables) ...
HiNT(Hi-C for copyNumber variation andTranslocation detection), a computational method to detect CNVs and Translocations from Hi-C data. HiNT has three main components:HiNT-PRE,HiNT-CNV, andHiNT-TL. HiNT-PRE preprocesses Hi-C data and computes the contact matrix, which stores contact frequencie...
HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterati...
peakFiles 我们可以循环遍历我们的制表符分隔文件（伪装成 .xls 函数）并使用循环将它们作为 data.frames...
1. Raw data We usedRao's HiCdata from GEO. Take thedatain GM12878 cell line as example. The string variableroot_dirdefined inall_parser.pydetermines the directory storing all raw and processed data. Here we unzip Hi-C data into/data/RaoHiC/raw/GM12878.root_dircould be customized accordi...
HiC-DC+ also enables differential analysis of Hi-C or HiChIP interactions between a pair of conditions, given replicate experiments. To do this, HiC-DC+ estimates genomic distance-dependent scaling factors from the data and uses DESeq2 to assess the significance of differential interactions (Method...