Software:Article Title: Chromosome structure modeling tools and their evaluation in bacteria.
Article Snippet: Moreover, the default parameter configuration of some algorithms may be suboptimal D ow nloaded from https://academ ic.oup.com /bib/article/25/2/bbae044/7611922 by guest on 17 July 2024 Table 1: Information on the software tools for chromosome 3D structure reconstruction Software Availability Programing language Installation dependency Sampling algorithm Input data Output format Output structures EVR [66] Yes C, Python Python; numpy; scipy Error-vector resultant algorithm Hi-C contact matrix 3D coordinates; pdb file format Consensus FLAMINGO [67] Yes R R; parallel; mgcv; Matrix; prodlim; nlme Low-rank matrix completion algorithm Hi-C contact matrix 3D coordinates; txt file format Consensus GEM [57] Yes Matlab MATLAB Compiler Adaptive gradient descent method Hi-C contact matrix; genomic loci file 3D coordinates; txt file format Ensemble LorDG [52] Yes Java Java Gradient ascent Hi-C contact matrix 3D coordinates; pdb file format Ensemble miniMDS [68] Yes Python Matplotlib; numpy; pymp-pypi; scikit-learn; scipy MDS approximation algorithm and Kabsch algorithm Hi–C contact matrix 3D coordinates; tsv file format Consensus MOGEN [54] Yes Java Java Gradient ascent Hi-C contact matrix 3D coordinates; pdb file format Ensemble sBIF [69] Yes C++ CMake Gradient ascent Hi-C contact matrix 3D coordinates; txt file format Ensemble ShNeigh [70] Yes Matlab MATLAB compiler Shortest-path Floyd-Warshall algorithm and local proximity modeling Hi-C contact matrix 3D coordinates; txt file format Consensus ShRec3D [71] Yes Matlab MATLAB compiler Shortest-path Floyd-Warshall algorithm Hi-C contact matrix 3D coordinates; xyz file format Consensus SIMBA3D [72] Yes Python Numpy; scipy BFGS method with analytical gradient Hi-C contact matrix json file format Consensus Pastis [35] Yes Python Python; numpy; scipy; scikit-learn; pandas Optimization (MDS1, MDS2) and probabilistic modeling (PM1, PM2) Hi-C contact matrix 3D coordinates; pdb file format Consensus TADbit [73] Yes Python Matplotlib; numpy; scipy Simulated annealing and Monte Carlo sampling Hi-C contact matrix 3D coordinates; txt file format Ensemble 3DMax [55] Yes Java, Matlab Iava or MATLAB compiler Gradient ascent Hi-C contact matrix 3D coordinates; pdb file format Ensemble Note: Output structures (column 8): ‘Consensus’-based methods generate a single structure from the entire Hi-C dataset; ‘Ensemble’-based methods generate multiple 3D structures that satisfy the constraints from Hi-C data. for bacterial chromosome modeling, which may also contribute to their weaker correlations.
Sampling:Article Title: Chromosome structure modeling tools and their evaluation in bacteria.
Article Snippet: Moreover, the default parameter configuration of some algorithms may be suboptimal D ow nloaded from https://academ ic.oup.com /bib/article/25/2/bbae044/7611922 by guest on 17 July 2024 Table 1: Information on the software tools for chromosome 3D structure reconstruction Software Availability Programing language Installation dependency Sampling algorithm Input data Output format Output structures EVR [66] Yes C, Python Python; numpy; scipy Error-vector resultant algorithm Hi-C contact matrix 3D coordinates; pdb file format Consensus FLAMINGO [67] Yes R R; parallel; mgcv; Matrix; prodlim; nlme Low-rank matrix completion algorithm Hi-C contact matrix 3D coordinates; txt file format Consensus GEM [57] Yes Matlab MATLAB Compiler Adaptive gradient descent method Hi-C contact matrix; genomic loci file 3D coordinates; txt file format Ensemble LorDG [52] Yes Java Java Gradient ascent Hi-C contact matrix 3D coordinates; pdb file format Ensemble miniMDS [68] Yes Python Matplotlib; numpy; pymp-pypi; scikit-learn; scipy MDS approximation algorithm and Kabsch algorithm Hi–C contact matrix 3D coordinates; tsv file format Consensus MOGEN [54] Yes Java Java Gradient ascent Hi-C contact matrix 3D coordinates; pdb file format Ensemble sBIF [69] Yes C++ CMake Gradient ascent Hi-C contact matrix 3D coordinates; txt file format Ensemble ShNeigh [70] Yes Matlab MATLAB compiler Shortest-path Floyd-Warshall algorithm and local proximity modeling Hi-C contact matrix 3D coordinates; txt file format Consensus ShRec3D [71] Yes Matlab MATLAB compiler Shortest-path Floyd-Warshall algorithm Hi-C contact matrix 3D coordinates; xyz file format Consensus SIMBA3D [72] Yes Python Numpy; scipy BFGS method with analytical gradient Hi-C contact matrix json file format Consensus Pastis [35] Yes Python Python; numpy; scipy; scikit-learn; pandas Optimization (MDS1, MDS2) and probabilistic modeling (PM1, PM2) Hi-C contact matrix 3D coordinates; pdb file format Consensus TADbit [73] Yes Python Matplotlib; numpy; scipy Simulated annealing and Monte Carlo sampling Hi-C contact matrix 3D coordinates; txt file format Ensemble 3DMax [55] Yes Java, Matlab Iava or MATLAB compiler Gradient ascent Hi-C contact matrix 3D coordinates; pdb file format Ensemble Note: Output structures (column 8): ‘Consensus’-based methods generate a single structure from the entire Hi-C dataset; ‘Ensemble’-based methods generate multiple 3D structures that satisfy the constraints from Hi-C data. for bacterial chromosome modeling, which may also contribute to their weaker correlations.
Hi-C:Article Title: Chromosome structure modeling tools and their evaluation in bacteria.
Article Snippet: Moreover, the default parameter configuration of some algorithms may be suboptimal D ow nloaded from https://academ ic.oup.com /bib/article/25/2/bbae044/7611922 by guest on 17 July 2024 Table 1: Information on the software tools for chromosome 3D structure reconstruction Software Availability Programing language Installation dependency Sampling algorithm Input data Output format Output structures EVR [66] Yes C, Python Python; numpy; scipy Error-vector resultant algorithm Hi-C contact matrix 3D coordinates; pdb file format Consensus FLAMINGO [67] Yes R R; parallel; mgcv; Matrix; prodlim; nlme Low-rank matrix completion algorithm Hi-C contact matrix 3D coordinates; txt file format Consensus GEM [57] Yes Matlab MATLAB Compiler Adaptive gradient descent method Hi-C contact matrix; genomic loci file 3D coordinates; txt file format Ensemble LorDG [52] Yes Java Java Gradient ascent Hi-C contact matrix 3D coordinates; pdb file format Ensemble miniMDS [68] Yes Python Matplotlib; numpy; pymp-pypi; scikit-learn; scipy MDS approximation algorithm and Kabsch algorithm Hi–C contact matrix 3D coordinates; tsv file format Consensus MOGEN [54] Yes Java Java Gradient ascent Hi-C contact matrix 3D coordinates; pdb file format Ensemble sBIF [69] Yes C++ CMake Gradient ascent Hi-C contact matrix 3D coordinates; txt file format Ensemble ShNeigh [70] Yes Matlab MATLAB compiler Shortest-path Floyd-Warshall algorithm and local proximity modeling Hi-C contact matrix 3D coordinates; txt file format Consensus ShRec3D [71] Yes Matlab MATLAB compiler Shortest-path Floyd-Warshall algorithm Hi-C contact matrix 3D coordinates; xyz file format Consensus SIMBA3D [72] Yes Python Numpy; scipy BFGS method with analytical gradient Hi-C contact matrix json file format Consensus Pastis [35] Yes Python Python; numpy; scipy; scikit-learn; pandas Optimization (MDS1, MDS2) and probabilistic modeling (PM1, PM2) Hi-C contact matrix 3D coordinates; pdb file format Consensus TADbit [73] Yes Python Matplotlib; numpy; scipy Simulated annealing and Monte Carlo sampling Hi-C contact matrix 3D coordinates; txt file format Ensemble 3DMax [55] Yes Java, Matlab Iava or MATLAB compiler Gradient ascent Hi-C contact matrix 3D coordinates; pdb file format Ensemble Note: Output structures (column 8): ‘Consensus’-based methods generate a single structure from the entire Hi-C dataset; ‘Ensemble’-based methods generate multiple 3D structures that satisfy the constraints from Hi-C data. for bacterial chromosome modeling, which may also contribute to their weaker correlations.
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