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  1. 4681
    por Patil, Arun H, Halushka, Marc K
    Publicado 2021
    “…We present miRge3.0 that provides additional features along with compatibility to newer versions of Cutadapt and Python. The revisions of the tool include the ability to process Unique Molecular Identifiers (UMIs) to account for PCR duplicates while quantifying miRNAs in the datasets, correct erroneous single base substitutions in miRNAs with miREC and an accurate mirGFF3 formatted isomiR tool. miRge3.0 also has speed improvements benchmarked to miRge2.0, Chimira and sRNAbench. …”
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    Online Artículo Texto
    miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline
  2. 4682
    “…AVAILABILITY AND IMPLEMENTATION: Python3 code is available on GitHub at https://github.com/DanNissley/Compare-ribosome-occupancy. …”
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    Online Artículo Texto
    Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains
  3. 4683
    por LEHRER, STEVEN, RHEINSTEIN, PETER H.
    Publicado 2021
    “…The UK Biobank Data Parser (ukbb_parser) was used, a python-based package that allows easy interfacing with the large UK Biobank dataset. …”
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    Online Artículo Texto
    Common drugs, vitamins, nutritional supplements and COVID-19 mortality
  4. 4684
    “…A key feature of OpenABM-Covid19 are its Python and R interfaces, which has allowed scientists and policymakers to simulate dynamic packages of interventions and help compare options to suppress the COVID-19 epidemic.…”
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    Online Artículo Texto
    OpenABM-Covid19—An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing
  5. 4685
    “…METHODS: We used a data set consisting of news articles published on the Canadian Broadcasting Corporation (CBC) website between December 2019 and May 2020. We then used Python software to analyze the data using Latent Dirichlet Allocation topic modelling. …”
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    The Role of the Canadian Media During the Initial Response to the COVID-19 Pandemic: A Topic Modelling Approach Using Canadian Broadcasting Corporation News Articles
  6. 4686
    “…AVAILABILITY AND IMPLEMENTATION: We provide Python code and data for EPP-HMCNF and other models in a repository termed EPP (Enzyme Promiscuity Prediction) at https://github.com/hassounlab/EPP. …”
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    Online Artículo Texto
    Enzyme promiscuity prediction using hierarchy-informed multi-label classification
  7. 4687
    “…Statistical parametric mapping (SPM) was calculated using SPM1D in a Python package that offered a high-level interface to SPM1D. …”
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    Online Artículo Texto
    The Application of Statistical Parametric Mapping to Evaluate Differences in Topspin Backhand between Chinese and Polish Female Table Tennis Players
  8. 4688
    “…These interventions can incorporate the effects of delays, loss-to-follow-up, micro-targeting, and other factors. Implemented in pure Python, Covasim has been designed with equal emphasis on performance, ease of use, and flexibility: realistic and highly customized scenarios can be run on a standard laptop in under a minute. …”
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    Covasim: An agent-based model of COVID-19 dynamics and interventions
  9. 4689
    “…To address these issues, we developed an easy-to-use software package, PhyloFisher (https://github.com/TheBrownLab/PhyloFisher), written in Python 3. PhyloFisher includes a manually curated database of 240 protein-coding genes from 304 eukaryotic taxa covering known eukaryotic diversity, a novel tool for ortholog selection, and utilities that will perform diverse analyses required by state-of-the-art phylogenomic investigations. …”
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    Online Artículo Texto
    PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
  10. 4690
    “…This study presents the use of a decision tree (DT), an artificial neural network (ANN), bagging, and gradient boosting (GB) to forecast the compressive strength of concrete at high temperatures on the basis of 207 data points. Python coding in Anaconda navigator software was used to run the selected models. …”
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    Online Artículo Texto
    Comparative Study of Supervised Machine Learning Algorithms for Predicting the Compressive Strength of Concrete at High Temperature
  11. 4691
    “…For any enquiry about usage or installation feel free to contact the corresponding author, a Python module specifically designed for the visualisation of Plutchik’s emotions in texts or in corpora. …”
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    PyPlutchik: Visualising and comparing emotion-annotated corpora
  12. 4692
    “…The methods are available as an open-source software package called AmoePy, a Python-based toolbox for analyzing amoeboid cell motility (based on time-lapse microscopy data), including a graphical user interface and detailed documentation. …”
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    Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows
  13. 4693
    “…The provided implementation is easy to use and extends the python library, allowing the generation of interaction matrices and their manipulation (reading and writing as well as producing the average 2D-SIFt). …”
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    2D SIFt: a matrix of ligand-receptor interactions
  14. 4694
    “…Methods: In February 2020, we used Python to web-scrape the 250 most recent posts that mentioned abortion, removing all identifying information and usernames. …”
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    Real-Time Effects of Payer Restrictions on Reproductive Healthcare: A Qualitative Analysis of Cost-Related Barriers and Their Consequences among U.S. Abortion Seekers on Reddit
  15. 4695
    “…The algorithms were implemented in Python using OpenCV library. The green channel presented the highest number of correct matches in all methods. …”
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    Online Artículo Texto
    Comparative Analysis of Detectors and Feature Descriptors for Multispectral Image Matching in Rice Crops
  16. 4696
    “…AVAILABILITYAND IMPLEMENTATION: OMAmer is available from the Python Package Index (as omamer), with the source code and a precomputed database available at https://github.com/DessimozLab/omamer. …”
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    OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches
  17. 4697
    por Petrov, Drazen
    Publicado 2021
    “…Importantly, this toolkit is made available online as an open-source Python package (https://github.com/drazen-petrov/SMArt).…”
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    Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder
  18. 4698
    “…We show for both low- and high-background data sets that dropkick's weakly supervised model reliably learns which genes are enriched in ambient barcodes and draws a multidimensional boundary that is more robust to data set–specific variation than existing filtering approaches. dropkick provides a fast, automated tool for reproducible cell identification from scRNA-seq data that is critical to downstream analysis and compatible with popular single-cell Python packages.…”
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    Automated quality control and cell identification of droplet-based single-cell data using dropkick
  19. 4699
    “…Since the manual recognition and quantification of glomeruli on digital images is a challenging and time-consuming task, we generated a program in Python able to identify glomeruli in digital images and quantify their properties, such as size, number, and pixel intensity. …”
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    Online Artículo Texto
    Automated quantification of vomeronasal glomeruli number, size, and color composition after immunofluorescent staining
  20. 4700
    “…All data needed is loaded into a portable local database, which serves as an interface for well-known software frameworks. These include python-based Jupyter Notebooks and the use of RStudio projects and R markdown. …”
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    Online Artículo Texto
    NPARS—A Novel Approach to Address Accuracy and Reproducibility in Genomic Data Science
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