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  1. 5761
    “…CCH is implemented in Python and is freely available (as source code) from http://sourceforge.net/projects/cchsnp/. …”
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    Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies
  2. 5762
    “…ClinQC is written in Python with multiprocessing capability, run on all major operating systems and is available at https://sourceforge.net/projects/clinqc. …”
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    ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research
  3. 5763
    “…The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. …”
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    NeisseriaBase: a specialised Neisseria genomic resource and analysis platform
  4. 5764
    “…The VDJML file format specification is accompanied by a support library, written in C++ and Python, for reading and writing the VDJML file format. …”
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    VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements
  5. 5765
    “…Motif discovery was carried out using the MEME software, sequence identity calculation was done using an in-house Python script, multiple sequence alignments were performed using PROMALS3D and TCOFFEE tools, and phylogenetic tree calculations were performed using MEGA vs 7.0 tool. …”
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    Aminoacyl tRNA synthetases as malarial drug targets: a comparative bioinformatics study
  6. 5766
    “…We utilized the following tools and the development environments to develop VIADS: Django, Python, JavaScript, Vis.js, Graph.js, JQuery, Plotly, Chart.js, Unittest, R, and MySQL. …”
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    A visual interactive analytic tool for filtering and summarizing large health data sets coded with hierarchical terminologies (VIADS)
  7. 5767
    “…All statistical analysis methods were performed with this statistical software including Python version 3.6.1, R Software 3.5.1 and Excel 2011. …”
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    HPV genotype prevalence and distribution during 2009–2018 in Xinjiang, China: baseline surveys prior to mass HPV vaccination
  8. 5768
    “…Data analysis is done using programming language R and Python. METHODS: We first quantify edge-weights of the miRNA-mRNA pairs by combining their expression correlation coefficient in tumor (T_CC) and correlation coefficient in normal (N_CC). …”
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    Clustering analysis of microRNA and mRNA expression data from TCGA using maximum edge-weighted matching algorithms
  9. 5769
    “…METHODS: We developed the Python-based MycTB Genome to Test (MTBGT) tool that transforms WGS-derived data into laboratory-validated results of the primary RDTs—Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, and GenoscholarNTM+MDRTB II. …”
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    Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data
  10. 5770
    “…The methodology could prove to be a particularly useful tool for ARG surveillance and the assessment of the effectiveness of strategies for mitigating the spread of antibiotic resistance. The python package is hosted in the Git repository: https://github.com/gaarangoa/ExtrARG ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40168-019-0735-1) contains supplementary material, which is available to authorized users.…”
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    Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm
  11. 5771
    “…After completing natural language processing of the Korean language, a morphological analyzer, we performed topic modeling using latent Dirichlet allocation (LDA) in the Python library, Gensim. A 10-topic model was selected and run with 3000 Gibbs sampling iterations to fit the model. …”
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    Mining Hidden Knowledge About Illegal Compensation for Occupational Injury: Topic Model Approach
  12. 5772
    “…In conclusion, the machine learning is an efficient method to confirm the important role of PTH and BALP mixed with nutritional conditions for fetal bone growth performance of goats. All the Python scripts including results and comments are available into an open repository at https://gitlab.com/muntisa/goat-bones-machine-learning.…”
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    Machine learning classification models for fetal skeletal development performance prediction using maternal bone metabolic proteins in goats
  13. 5773
    “…METHODS: The tool performs an unbiased and automated search of the NCBI database, collects relevant genomic sequences based on user-defined Taxon-ID and executes a Python program to discard synthetic sequences. A profile of primer-probe sequence complementarity to targets is then generated. …”
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    1786. An Automated Method to Assess Oligonucleotide Primer and Probe Complementarity to Genomic Targets in Infectious Disease qPCR Assays
  14. 5774
    “…A local database of 22 TA homologs was created for Cronobacter sakazakii and a Python version 3 shell script was generated to extract TA FASTA sequences present in 234 C. sakazakii genomes previously sequenced as part of Center for Food Safety and Applied Nutrition’s (CFSAN) GenomeTrakr project. …”
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    Prevalence, Distribution, and Phylogeny of Type Two Toxin-Antitoxin Genes Possessed by Cronobacter Species where C. sakazakii Homologs Follow Sequence Type Lineages
  15. 5775
    “…Moreover, we show how we increased the throughput of our Walz IMAGING-PAM, also found in many other departments around the world. We have designed a Python and R-based open source toolkit that allows for semi-automated sample segmentation and data analysis thereby reducing the processing bottleneck of large experimental datasets. …”
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    Fluctuating light experiments and semi-automated plant phenotyping enabled by self-built growth racks and simple upgrades to the IMAGING-PAM
  16. 5776
    “…The software and data are freely available from GitHub (https://github.com/dlcarper/DISCo-microbe) and Python Package Index (PYPI).…”
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    DISCo-microbe: design of an identifiable synthetic community of microbes
  17. 5777
    “…RESULTS: To select species-specific sequences or genes, a total of 180 Lactobacillus genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S–23S rRNA gene. …”
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    Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate
  18. 5778
    “…The navigation data were collected by request through an application-programming-interface using a web crawler (web data extraction tool) in Python. The shortest driving time and distance were extracted from the navigation data. …”
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    Measuring spatial accessibility and within-province disparities in accessibility to county hospitals in Shaanxi Province of Western China based on web mapping navigation data
  19. 5779
    “…Aspideretes gangeticus, A. hurum, Eublepharis macularius, Varanus bengalensis, Python molurus, Eryx johnii, Ptyas mucosus mucosus, Daboia russelii russelii and five fish species including Hypophthalmichthys molitrix, Cirrhinus reba, Labeo dero, Mastacembelus armatus, and Pethia ticto were reported for the first time from this region. …”
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    The use of fish and herptiles in traditional folk therapies in three districts of Chenab riverine area in Punjab, Pakistan
  20. 5780
    “…Given that the QSAR models we used to compute the QAFFP were selected on the basis of data availability alone, we anticipate better modeling results for QAFFP generated using more diverse and biologically meaningful targets. Data sets and Python code are publicly available at https://github.com/isidroc/QAFFP_regression.…”
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    QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction
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