In this section, we discuss some disadvantages of DP and our methods, which may cause the methods fail to give good clustering results in some cases. We also give a brief discussion on the parameter selection of Density Peaks algorithm. Those assumptions of the DP algorithm rely on the uneven...
Clustering techniques are essential elements for exploring and analyzing data. This paper provides a comparative study between a new clustering algorithm based on a new density peak detection approach introducing the imprecise data concept, named Robust density peak detection with imprecision data (RDPTI...
Clusters, hexagonally arranged, form in the bulk at very small U0, behaving in the same way as unconfined clusters, with one of the hexagonal directions aligned with the walls, as confirmed by the study of the x-density, ρ(x), in panel g) which reveals separated peaks. This situation ...
The Common Chaffinch genome landscape is characterized by severalFstpeaks that coincide with valleys indxyand π, and negative peaks in Tajima’s D mainly in the continent (i.e., peaks in chromosomes 1,1 A, 2, 3, 4, 4 A, 6, Fig.5). This pattern is consistent with the model of re...
Intersecting our ChIP-seq peak sets with the 55,585 ATAC-seq peaks revealed a significant co-occurrence of ATAC-seq signal and both H3K4me3 signal (permutation test; 10,000 permutations, observed overlap: 15,465, permuted overlap: 2251, Z-score: 15,465,p-value < 0.0001, Fig.2i) and...
The introduction of the smoothed level density (sld) method represents a recent advancement in analyzing the multitude of shell effects during the fission process [24]. Applied to any type of mean field approximations the sld method focuses on the shell effects at the Fermi level of single parti...
All-against-all BLASTp analyses and subsequent orthology clustering of the predicted protein sequences of all five strains andL. capsiciAZ78 [4] resulted in a pangenome of 10,028 orthologous groups. The core genome consisted of 2,891 CDSs, representing 54 % of the CDSs of each strain (Fig...
Trend clustering analysis was performed on the union of DIMs (Fig. 3.e-n). Different plants exhibited relatively higher intensity of specific metabolites in the shoot. In cluster 1, the metabolites in P. elliottii and P. massoniana/P. elliottii showed relatively hi...
The clustering of cell types together by lineage based on chromatin state maps (Supplementary Fig. 10c) also supports the model that the landscape of active and repressed chromatin is established no later than lineage commitment, and that this landscape is a defining feature of each cell type. ...
An average linkage clustering approach was used to correct the redundancy of Ks values that correspond to GD events. The GD modes of each genome were estimated by MSCANX. Recently, duplicated genes (in-paralogs) along T. asiatica and T. saginata that arise after their divergence were ...