“…This composite of fat and ligaments is hypothesized to serve a shock-absorbing, stabilizing function for the sacroiliac joint and the lumbopelvic transition region. Using a novel Python-based software (VolSEQ), total PSIJ volume and fat volume were computed semi-automatically. …”
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“…AVAILABILITY AND IMPLEMENTATION: MuDCoD is publicly available at https://github.com/bo1929/MuDCoD as a Python package. Implementation includes simulation and real-data experiments together with extensive documentation.…”
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“…These tools are delivered as easy to use python libraries, command line tools, Common Workflow Language Tools, and as Web Image Processing Pipeline interactive plugins to ensure a wide range of users can access and use them. …”
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“…Eight machine learning classifiers were employed on a total weighted sample of 5819 women and evaluated using performance metrics to predict and identify important predictors of unmet need of family planning with Python 3.10 version software. Data preparation techniques such as removing outliers, handling missing values, handling unbalanced categories, feature engineering, and data splitting were applied to smooth the data for further analysis. …”
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“…While the fragility indices have intuitive appeal and have been widely applied, their behavior across a wide range of contingency tables has not been rigorously evaluated. Methods Using a Python software program, a simulation approach was employed to generate random 2x2 contingency tables. …”
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“…The shape of the anatomical cross-sectional areas of the hamstrings and quadriceps in three leg positionings were compared by fitting ellipsoidal functions to the segmented MRI data and calculating the so-called J index for every image slice using the Python scripting language. Different levels of knee elevation resulted in apparent changes in J index for all muscles except vastus medialis. …”
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“…Radiomic features were extracted by drawing the region of interest using the 3D slicer image computing platform and Python. Key features were selected through LASSO, and the radiomics score (Rad-score) was calculated. …”
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“…A reference implementation of FCCD in Python is available as supplementary information.…”
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“…A reference implementation using Oracle 11 g database and the Python framework, Django is presented. CONCLUSIONS: By focusing on a minimal feature set and a modular design we have been able to deploy the BonsaiLIMS system very quickly. …”
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“…The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. Benchmarking was performed using either a dinucleotide or codon substitution model applied to an alignment of BRCA1 sequences from 20 mammals, or a 10 species subset. …”
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“…It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. …”
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“…SRST is open-source, requires Python, BWA and SamTools, and is available from http://srst.sourceforge.net.…”
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“…The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. …”
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“…They are particularly well adapted for searching 3’ alternative poly-adenylation events and can be also useful for studying the structure of transcriptional networks. The PSAWNpy, (in Python) and PSAWNml (in Matlab) programmes are freely available and can be downloaded at http://code.google.com/p/arraymatic. …”
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“…RESULTS: We have developed pyBioImage, an open source cross platform image analysis software application, written in python with C extensions that is specifically tailored to the needs of immunologic research involving 4D imaging of GCs. …”
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“…Availability: mapDamage 2.0 is available at ginolhac.github.io/mapDamage/ as a Python package and documentation is maintained at the Centre for GeoGenetics Web site (geogenetics.ku.dk/publications/mapdamage2.0/). …”
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“…The ITEP toolkit consists of: (1) a series of modular command-line scripts for identification, comparison, curation, and analysis of protein families and their distribution across many genomes; (2) a set of Python libraries for programmatic access to the same data; and (3) pre-packaged scripts to perform common analysis workflows on a collection of genomes. …”
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“…The output gene sets may be used directly within GSEA and do not require knowledge of programming languages such as Perl, R or Python. The output sets can also be used with other analysis software such as ErmineJ that accept gene sets in the same format. …”
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“…Data clustering and the preparation of the input file for InCHlib is facilitated by the Python utility script inchlib_clust. CONCLUSIONS: The cluster heatmap is one of the most popular visualizations of large chemical and biomedical data sets originating, e.g., in high-throughput screening, genomics or transcriptomics experiments. …”
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“…Biological entities such as genes and proteins were tagged using ABNER, and processed using Python scripts to produce a list of putative biomarkers. …”
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