“…UNDR ROVER is implemented in Python and runs on all popular POSIX-like operating systems (Linux, OS X). …”
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“…RESULTS: TCGA Expedition software consists of a set of scripts written in Bash, Python and Java that download, extract, harmonize, version and store all TCGA data and metadata. …”
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“…The LASSIM method is implemented as a general-purpose toolbox using the PyGMO Python package to make the most of multicore computers and high performance clusters, and is available at https://gitlab.com/Gustafsson-lab/lassim. …”
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“…RESULTS: Our HRNN method was implemented with the Python language. It was first evaluated on simulated data representing linear and nonlinear time-delayed gene-gene interaction models across a range of network sizes and variances of noise. …”
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“…By repeating these analyses using bedtools, Galaxy and custom Python scripts, we show that the STQL solution is usually the simplest, and the parallel execution achieves significant speed-up with large data files. …”
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“…Phylogenetic analyses show that the non-mammalian viruses (expect the python, Morelia spilota, associated papillomavirus) cluster near the base of the papillomavirus evolutionary tree. …”
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“…LSTrAP is implemented in Python 3.4 (or higher) and available under MIT license from https://github.molgen.mpg.de/proost/LSTrAP ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-017-1861-z) contains supplementary material, which is available to authorized users.…”
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“…RESULTS: UGbS-Flex combines publicly available software with in-house python and perl scripts to efficiently call SNPs from genotyping-by-sequencing reads irrespective of the species’ ploidy level, breeding system and availability of a reference genome. …”
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“…RESULTS: We developed PRS-on-Spark (PRSoS), a software implemented in Apache Spark and Python that accommodates different data inputs and strand-ambiguous SNPs to calculate PRS. …”
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“…The rates are inferred using the previously published Tree Independent Generation of Evolutionary Rates (TIGER), and the partitioning is conducted using our novel python script RatePartitions. We conducted simulations to assess the performance of our new method, and we applied it to eight published multi-locus phylogenetic datasets, representing different taxonomic ranks within the insect order Lepidoptera (butterflies and moths) and one phylogenomic dataset, which included ultra-conserved elements as well as introns. …”
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“…Outcomes were analyzed by Kaplan–Meier and Cox regression analyses using Python (3.6.0) and R (3.4.0). RESULTS: We constructed a 4-gene signature (ACVR2A, APC, DOCK2, and POLE), with training in 45 hypermutated patients at ZJU and validation in 24 hypermutated patients from TCGA. …”
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“…SplicedFamAlign was implemented in Python. Source code is freely available at https://github.com/UdeS-CoBIUS/SpliceFamAlign. …”
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“…We developed data-acquisition workflows for Apache Storm and NiFi in Java and Python to capture patient monitoring and laboratory data for downstream analytics. …”
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“…DNAscan is implemented in Python. Its code and documentation are available on GitHub: https://github.com/KHP-Informatics/DNAscan. …”
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“…This work develops opens source software in Python to convert a database of semantic predications of all of PubMed's 27.9 million indexed abstracts into a semantic inference network and biomedical concept graph in Neo4j. …”
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“…Next, a logistic regression algorithm was applied to predict osteoporotic or non-osteoporotic vertebra. The Tensor flow and Python were used as the machine learning tools. The Tensor flow user interface developed in our institute was used for easy code generation. …”
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“…The web application was developed in Python using COBRApy and Django. Results: The proposed method was demonstrated to be robust enough to process even non-curated, incomplete, or imprecise metabolic networks, in addition to integrated host-pathogen models. …”
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“…SigProfilerMatrixGenerator is written in Python with an R wrapper package provided for users that prefer working in an R environment. …”
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“…We, then, implemented a novel recursive split-resubmit python program that searched for homologs of > 50 base pairs (bp), uncovering parts for a better exploitation of the datasets. …”
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“…CONCLUSIONS: We developed a new cell composition deconvolution method and the implementation was entirely based on the publicly available R and Python packages. In addition, we compiled a new set of reference gene expression profiles, which might allow for a more robust prediction of the immune cell fractions from the expression profiles of cell mixtures. …”
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