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  • Matlab scripts used to analyze data associated with the manuscript entitled "A single cell atlas of the human liver tumor microenvironment". *please used Matlab 2019b to run the following m files. Files: inputData.mat: mat contains all raw and preprocessed data used in the study Create_Interactions_Network.m: Matlab script used to calculate Ligand-Receptor interaction score between different cell types. The script creates panels of Figure 3 and Table S5. Hepatocytes_Reconstruction.m: Matlab script used to reconstruct human hepatocytes zonation along the lobule axis. The script creates panel 'c' of Figure 4, Figure S4, and Table S7. Cancer_Cells_Spatial_Analysis.m: Matlab script used to calculate differential gene expression between malignant cells found at different zones (malignant border, malignant core, and fibrotic zone) captured by laser microdissection. The script creates panel 'd' of Figure 4 helperFunctions.zip: This folder contains required functions used by the m files.
    Data Types:
    • Software/Code
  • This contains the scripts we used while mining git repositories to quantify and characterize three different types of "Ghost Commits": MG 1, MG 2, and FG.
    Data Types:
    • Software/Code
  • # Installation conda create -n deep_texture python=3.6 source activate deep_texture conda install numpy pillow conda install keras-gpu conda install keras # if GPUs are not available pip install git+https://github.com/keras-team/keras-applications.git@d506dc82d0 # downgrade keras-application ## usage import deep_texture (prep, dnn) = deep_texture.setup_texture(arch = 'nasnet', layer = 'normal_concat_11', cbp_dir = '/tmp') dtr = deep_texture.calc_features_file("./test.png", prep, dnn)
    Data Types:
    • Other
    • Software/Code
  • 1.0.0 - 2020-07-01 Feature Release This is a major revision of QSW_MPI. The focus of this release is the expansion of the simulation capabilities of QSW_MPI while focussing the scope of the package through the removal of features which are better supported through pre-existing alternatives (specifically file I/O and visualisation). Added Generalised support for quantum stochastic walks, including the non-moralising quantum stochastic walk through the qsw_mpi.MPI.LQSW and qsw_mpi.MPI.GQSW classes. Experimental support for sparse systems following the Gorini–Kossakowski–Sudarshan–Lindblad equation in its diagonalised form through the qsw_mpi.MPI.GKSL class. Support for MPI-enabled parallel output to HDF5 using H5Py via the non-user accessible module qsw_mpi.parallel_io. Additional operator types including the canonical Markov chain transition matrix, and those required for the demoralisation correction scheme. Changed All simulation types are now subclasses a generalised qsw_mpi.MPI.walk class. This breaks compatibility with version 0.0.1. qsw_mpi.MPI.walk.step and qsw_mpi.MPI.walk.series have been simplified, gathering of simulation results, or saving of the simulation results is now carried out through the qsw_mpi.MPI.walk.gather_result, qsw_mpi.MPI.walk.gather_populations, qsw_mpi.MPI.save_result or qsw_mpi.MPI.save_populations. Removed Removed visualisation module qsw_mpi.plot. For basic visualisation, direct use of Matplotlib and Networkx is recommended. Removed dedicated I/O module qsw_mpi.io. For HDF5 file operations, direct use of H5Py is recommended.
    Data Types:
    • Software/Code
  • Integrating data from multiple sources with the aim to identify records that correspond to the same entity is required in many real-world applications including healthcare, national security, and businesses. However, privacy and confidentiality concerns impede the sharing of personal identifying values to conduct linkage across different organizations. Privacy-preserving record linkage (PPRL) techniques have been developed to tackle this problem by performing clustering based on the similarity between encoded record values, such that each cluster contains (similar) records corresponding to one single entity. When employing PPRL on databases from multiple parties, one major challenge is the prohibitively large number of similarity comparisons required for clustering, especially when the number and size of databases are large. While there have been several private blocking methods proposed to reduce the number of comparisons, they fall short in providing an efficient and effective solution for linking multiple large databases. Further, all of these methods are largely dependent on data. In this paper, we propose a novel private blocking method for efficiently linking multiple databases by exploiting the data characteristics in the form of probabilistic signatures and introduce a local blocking evaluation step for validating blocking methods without knowing the ground-truth. Experimental results show the efficacy of our method in comparison to several state-of-the-art methods.
    Data Types:
    • Other
    • Software/Code
  • Abstract: Platinum dissolution and restructuring due to surface oxidation are primary degradation mechanisms that limit the lifetime of Pt-based electrocatalysts for electrochemical energy conversion. Here, we studied well-defined Pt(100) and Pt(111) electrode surfaces by in situ high-energy surface X-ray diffraction, on-line inductively coupled plasma mass spectrometry, and density functional theory calculations, to elucidate the atomic-scale mechanisms of these processes. The locations of the extracted Pt atoms after Pt(100) oxidation reveal distinct differences from the Pt(111) case, which explains the different surface stability. The evolution of a specific stripe oxide structure on Pt(100) produces unstable surface atoms which are prone to dissolution and restructuring, leading to one order of magnitude higher dissolution rates. Contents of this repository: The custom CTR calculation software datautils. The software is written in python and has dependencies, which are stated in the requirements.txt file. Using pip you should be able to easily install the package using pip install . inside the root directory of the package. This should also handle all requirements. An example for a CTR fit is given in the jupyter notebook in the example folder. The binoculars backend for the HESXRD data extraction.
    Data Types:
    • Software/Code
  • An Open Source, Parallel and Heterogeneous Finite Element Analysis Framework
    Data Types:
    • Software/Code
  • Publication release. Changed default setting for biallelic filter from off to on.
    Data Types:
    • Software/Code
  • LCIO v1.6.0 Diff since v1.5.0 Closed issues: register v1.4.3 (#39) add indexing to collections (#40)
    Data Types:
    • Software/Code
  • Big changes Add load_fastq_directory to builtin functions Enable specifying all module resources by URL with download on first use Other Better messages when using lock1 No longer ship JS libraries (also do not expand them in-place) Remove old motus/specI moduels Fix CIGAR reinjection bug (already fixed in v`1.1.1)
    Data Types:
    • Software/Code