Listed python codes of our algorithm with explanations (Python 3.9 recommended). by Takayuki Niizato (162226)

The most significant functions in seven gene sets. by Pengcheng Zhao (6009899)

Probably pathogenic variants (algorithms). by Felipe Fidalgo (642532)

Efficient algorithms to discover alterations with complementary functional association in cancer by Rebecca Sarto Basso (6728921)

“…Mutual exclusivity arises because of the complementarity, at the functional level, of alterations in genes which are part of a group (e.g., a <i>pathway</i>) performing a given function. …”

EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit by Gonzalo Colmenarejo (650249)

“…For a RDKit molecule, it provides (i) a PNG binary string with an image of the molecule with color-highlighted functional groups; (ii) a list of sets of atom indices (idx), each set corresponding to a functional group; (iii) a list of pseudo-SMILES canonicalized strings for the full functional groups; and (iv) a list of RDKit labeled mol objects, one for each full functional group. …”

Algorithm framework. by Zongjin Li (38031)

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Python-Based Algorithm for Estimating NRTL Model Parameters with UNIFAC Model Simulation Results by Se-Hee Jo (20554623)

“…This algorithm conducts a series of procedures: (1) fragmentation of the molecules into functional groups from SMILES, (2) calculation of activity coefficients under predetermined temperature and mole fraction conditions by employing universal quasi-chemical functional group activity coefficient (UNIFAC) model, and (3) regression of NRTL model parameters by employing UNIFAC model simulation results in the differential evolution algorithm (DEA) and Nelder–Mead method (NMM). …”

MSVM-RFE algorithm for screening key genes. by Ya xi Zhu (11624730)

<b>Opti2Phase</b>: Python scripts for two-stage focal reducer by Morgan Najera (21540776)

“…</li></ul><p dir="ltr">The scripts rely on the following Python packages. Where available, repository links are provided:</p><ol><li><b>NumPy</b>, version 1.22.1</li><li><b>SciPy</b>, version 1.7.3</li><li><b>PyGAD</b>, version 3.0.1 — https://pygad.readthedocs.io/en/latest/#</li><li><b>bees-algorithm</b>, version 1.0.2 — https://pypi.org/project/bees-algorithm</li><li><b>KrakenOS</b>, version 1.0.0.19 — https://github.com/Garchupiter/Kraken-Optical-Simulator</li><li><b>matplotlib</b>, version 3.5.2</li></ol><p dir="ltr">All scripts are modular and organized to reflect the design stages described in the manuscript.…”

Python-based Monte Carlo Simulation Tool by Yangfan Jiang (9372782)

FAR-1: A Fast Integer Reduction Algorithm Compared to Collatz and Half-Collatz by Faizan Ali (21689861)

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Gene content overlap in <i>RNF43 G659fs</i> mutation-specific pathways. by Alexis M. Thornton (11068403)

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The eVIP algorithm uses RNA-seq data to predict the function of somatic mutations. by Alexis M. Thornton (11068403)

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Algorithmic assessment reveals functional implications of GABRD gene variants linked to idiopathic generalized epilepsy by Ayla Arslan (17943365)

“…</p> <p>The study employs a combination of in silico algorithms to analyze 82 variants of unknown clinical significance of GABRD gene sourced from the ClinVar database. …”

Data_Sheet_1_Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways.zip by Maxim Sorokin (4379848)

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The results of LASSO regression algorithm. by Xue Fu (549661)

Top-ranked hub genes identified by 5 cytoHubba algorithms. by Jun Li (6494)

Performance of ENQUIRE’s gene normalization algorithm. by Luca Musella (19986312)

Average quality scores of the models of the analysis set as a function of the <i>w</i>_<i>SP</i> with which the DOPE potential has been included in the objective function... by Giacomo Janson (8138517)

An expectation-maximization algorithm for finding noninvadable stationary states. by Robert Marsland (8616483)

“…<i>(b)</i> Metabolic byproducts move the relevant unperturbed state from <b>R</b>⁰ (gray ‘x’) to (black ‘x’), which is itself a function of the current environmental conditions. …”