Topologically associating domains (TADs) are critical structural units in three-dimensional genome organization of mammalian genome. Dynamic reorganizations of TADs between health and disease states are associated with essential genome functions. However, computational methods for identifying reorganized TADs ar...
We have performed a systematic analysis of gene identification in genomic sequence by similarity search against expressed sequence tags (ESTs) to assess th... LC Bailey,DB Searls,GC Overton - 《Genome Research》 被引量: 218发表: 1998年 Three-mode principal components analysis: choosing the number...
Minimum abundance of an isoform to include in differential expression tests, specified as a scalar between 0 and 1. For alternative isoforms quantified at below the specified value, the function rounds down the abundance to zero. The specified value is a fraction of the major isoform. The functi...
Summary A method for identifying pattern changes between 2 experimental conditions in correlation networks (e.g., gene co-expression networks), which builds on a commonly used association measure, such as Pearson's correlation coefficient. This package includes functions to calculate correlation matrices...
However, these measures lose the information of what exactly makes the difference between the motifs of interest. Hence, the comparison of multiple pairs of motifs can result in similar measures. There are various tools for the analysis and visualization of motifs as summarized in Table 1. The ...
1e-5(default) |scalar between0and1 MultiReadCorrection—Flag to improve abundance estimation using rescue method false(default) |true NormalizeCompatibleHits—Flag to use only fragments compatible with reference transcript to calculate FPKM values ...
It utilizes two steps to estimate the conditional essentiality for each gene in the genome. First, it collects evidence of conditional essentiality for each insertion by comparing read counts of that insertion between conditions. Second, it combines insertion-level evidence for the corresponding gene....
However , people in the south are als o more rulnerable to certain blood-borne illness es , as they lack the genes to stop them .Genes can also cause physical differences between northerners an d southerners . Most n ortherners have the ABCC11 gene, which cau ses dry carwar (耳 ),...
Chromosomal Mapping The conformation of the genome in the nucleus and contacts between both proximal and distal loci influence gene expression. In order to map genomic contacts, Lieberman-Aiden et al. (p. 289 , see the cover) developed a technique to allow the detection of all interactions betw...
their strength and how they are regulated between the two conditions of interest. To facilitate the interpretation of these results, we implemented an over-representation test to determine the dominant variations at the gene, cell-type or functional level. In addition, the package provides several ...