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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
  • # 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
  • 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
  • This code enables the mapping of single-molecule m6A methylations.
    Data Types:
    • Software/Code
  • ATC-Anno is an annotation tool for the transcription and semantic annotation of air traffic control utterances. It was developed at the Spoken Language Systems (LSV) group at Saarland University. The latest version of the tool can always be found on the LSV GitHub account. If you use the tool in your research, please cite the associated paper: Marc Schulder, Johannah O'Mahony, Yury Bakanouski, Dietrich Klakow (2020). ATC-Anno: Semantic Annotation for Air Traffic Control with Assistive Auto-Annotation. In Proceedings of the International Conference on Language Resources and Evaluation (LREC), Marseilles, France.
    Data Types:
    • Other
    • Software/Code
  • This is the software and data set named "Supplementary Software 1" for the research paper "Reaching the era of subsidy free offshore wind". Please refer to the README file in the ZIP file for instructions. The paper is currently under review and access is for peer-review purposes only.
    Data Types:
    • Software/Code
  • MATLAB codes used to model arsenic(III) remediation using a composite TiO2-Fe2O3 sorbent in batch and continuous-flow systems, using a modified form of the pseudo-second order (PSO) adsorption kinetic model. This data supports the manuscript provisionally titled 'A kinetic adsorption model to inform the design of arsenic(III) treatment plants using photocatalyst-sorbent materials'
    Data Types:
    • Software/Code
  • Tools for interacting with the publicly available California Delta Fish Salvage Database, including continuous deployment of data access, analysis, and presentation.
    Data Types:
    • Software/Code
  • Contains some fixes as preparation for the reproducability review.
    Data Types:
    • Software/Code
  • RDF dump of wikidata produced with wdumps. View on wdumper entity count: 0, statement count: 0, triple count: 0
    Data Types:
    • Software/Code
    • Dataset
    • File Set