Table6_Natural and artificial selection of multiple alleles revealed through genomic analyses.xlsx by Jana Biová (11287971)

“…We tested and validated the algorithm and presented the utilization of MADis in a pod pigmentation L1 gene case study with multiple CMs from natural or artificial selection. …”

Table1_Natural and artificial selection of multiple alleles revealed through genomic analyses.DOCX by Jana Biová (11287971)

“…We tested and validated the algorithm and presented the utilization of MADis in a pod pigmentation L1 gene case study with multiple CMs from natural or artificial selection. …”

GameOfLife Prediction Dataset by David Towers (12857447)

“…Excluding 0, the lower numbers also get increasingly unlikely, though more likely than higher numbers, we wanted to prevent gaps and therefore limited to 25 contiguous classes</p><p dir="ltr">NumPy (.npy) files can be opened through the NumPy Python library, using the `numpy.load()` function by inputting the path to the file into the function as a parameter. …”

Investigation of cardiac mechanics and mechanical circulatory support therapies in peripartum cardiomyopathy using machine learning and patient-specific computational modelling by Juliet Nagawa (17333779)

“…</li></ul><p dir="ltr"> <b>ANN.zip</b></p><ul><li>Matlab and Python programs used to develop machine learning algorithms and developed machine learning models.…”

Code and data for evaluating oil spill amount from text-form incident information by Yiming Liu (18823387)

“…These are separately stored in the folders “description” and “posts”.</p><h2>Algorithms for Evaluating Release Amount (RA)</h2><p dir="ltr">The algorithms are split into the following three notebooks based on their functions:</p><ol><li><b>"1_RA_extraction.ipynb"</b>:</li><li><ul><li>Identifies oil spill-related incidents from raw incident data.…”

COI reference sequences from BOLD DB by John Sundh (12853901)

“…<br>The file bold_clustered.sintax.fasta.gz is directly compatible with the SINTAX algorithm in vsearch while files bold_clustered.assignTaxonomy.fasta.gz and bold_clustered.addSpecies.fasta.gz are directly compatible with the assignTaxonomy and addSpecies functions from DADA2, respectively. …”

Inflammation-Associated Stromal Reprogramming Can Initiate Metaplasia and Facilitate Dysplastic Progression via ECM by Deng Pan (47215)

“…_csr.csr_matrix<br>X.dtype == 'float32'</p><p><br></p><p dir="ltr">AnnData.obs<br>===========</p><p dir="ltr">index - cell barcodes + sample_diagnosis<br>samplename - coded sample ID<br>n_genes - number of measured genes in the cell<br>n_molecules - number of molecules sequenced<br>doublet_score - whether the droplet contained two cells (scrublet)<br>percent_mito - percent of genes measured that are mitochondrial<br>leiden - cluster labels from leiden algorithm<br>louvain - cluster labels from the louvain algorithm<br>nobatch_leiden - non-batch corrected leiden cluster labels<br>nobatch_louvain - non-batch corrected louvain cluster labels<br>diagnosis - tissue diagnosis, N normal, M metaplasia, D dysplasia, T tumor<br>phase - cell cycle phase<br>sample_diagnosis - sample ID + tissue diagnosis<br>patient - patient ID<br>treatment - whether the patient recieved any treatment<br>procedure - how the sample was aquired<br>hcl_refined - human cell landscape refined cell type name<br>hcl_celltype - human cell landscape cell type best match<br>hcl_score - human cell landscape matching score<br>CLid - cell ontology ID<br>CL_name - cell ontology cell type name</p><p><br></p><p dir="ltr"><br></p><p dir="ltr">AnnData.var<br>===========</p><p dir="ltr">index - gene symbols<br>gene_ids - ensembl gene IDs<br>feature_types - type of the feature<br>genome - genome build<br>is_mito - whether the gene is mitochondrial<br>is_ribo - whether the gene is ribosomal</p><p dir="ltr"><br></p><p dir="ltr">AnnData_embeddings:<br>========================</p><p dir="ltr">PCA (obsm.X_pca)<br>UMAP (obsm.X_umap)<br>PCA_nobatch (obsm.X_pca_original)<br>UMAP_nobatch (obsm.X_umap_nobatch)<br>neighbors (AnnData.uns)</p><p dir="ltr"><br></p><p><br></p><p dir="ltr">Marker Genes:<br>=============<br>AnnData.uns['rank_genes_groups_filtered'].keys()</p><p dir="ltr">names - one list per leiden cluster<br>logfoldchanges - one cluster vs all others</p><p dir="ltr">scores - wilcoxon statistic<br>pvals - wilcoxon p-value</p><p dir="ltr">pvals_adj - BH adjusted p-values</p><p dir="ltr">params = {'corr_method': 'benjamini-hochberg', <br>'groupby': 'leiden',<br>'method': 'wilcoxon',<br>'reference': 'rest',<br>'use_raw': True}</p><p dir="ltr"><br></p>…”

An Automated Platform for Analysis of Phosphoproteomic Datasets:  Application to Kidney Collecting Duct Phosphoproteins by Jason D. Hoffert (502031)

“…In addition, the output files generated by this program are compatible with downstream phosphorylation site assignment using the Ascore algorithm, as well as phosphopeptide quantification via QUOIL. …”

An Automated Platform for Analysis of Phosphoproteomic Datasets:  Application to Kidney Collecting Duct Phosphoproteins by Jason D. Hoffert (502031)

“…In addition, the output files generated by this program are compatible with downstream phosphorylation site assignment using the Ascore algorithm, as well as phosphopeptide quantification via QUOIL. …”

An Automated Platform for Analysis of Phosphoproteomic Datasets:  Application to Kidney Collecting Duct Phosphoproteins by Jason D. Hoffert (502031)

“…In addition, the output files generated by this program are compatible with downstream phosphorylation site assignment using the Ascore algorithm, as well as phosphopeptide quantification via QUOIL. …”

An Automated Platform for Analysis of Phosphoproteomic Datasets:  Application to Kidney Collecting Duct Phosphoproteins by Jason D. Hoffert (502031)

“…In addition, the output files generated by this program are compatible with downstream phosphorylation site assignment using the Ascore algorithm, as well as phosphopeptide quantification via QUOIL. …”

Interaction of Rare-Earth Metals and Some Perfluorinated β‑Diketones by Maxim A. Lutoshkin (6651425)

“…Systems have been investigated spectrophotometrically using a multiwave nonlinear least-squares regression algorithm for data processing. Conditional stability constants were obtained for a wide pH region (2.0–5.4) at constant ionic strength (<i>I</i> = 0.5 M, NaCl). …”

An Automated Platform for Analysis of Phosphoproteomic Datasets:  Application to Kidney Collecting Duct Phosphoproteins by Jason D. Hoffert (502031)

“…In addition, the output files generated by this program are compatible with downstream phosphorylation site assignment using the Ascore algorithm, as well as phosphopeptide quantification via QUOIL. …”

BrainPepPass: all scripts by Ewerton de Oliveira (16033631)

“…</p> <p><br></p> <p>Obs: Among the compressed files, there is the sLE_functions.py script. This script is responsible for providing the necessary functions of the sLE algorithms to run BrainPepPass framework.…”

Spatiotemporal Soil Erosion Dataset for the Yarlung Tsangpo River Basin (1990–2100) by peng xin (21382394)

“…Bias correction was conducted using a 25-year baseline (1990–2014), with adjustments made monthly to correct for seasonal biases. The corrected bias functions were then applied to adjust the years (2020–2100) of daily rainfall data using the "ibicus" package, an open-source Python tool for bias adjustment and climate model evaluation. …”

CSPP instance by peixiang wang (19499344)

“…</b></p><p dir="ltr">Its primary function is to create structured datasets that simulate container terminal operations, which can then be used for developing, testing, and benchmarking optimization algorithms (e.g., for yard stacking strategies, vessel stowage planning).…”

SParse EXact (SPEX) LU and Cholesky Factorization Library by Erick Moreno-Centeno (19460626)

“…., in computing radial basis functions for scattered data interpolation), and engineering (e.g., in studies of anharmonic oscillations in semiconductors). …”

UMAHand: Hand Activity Dataset (Universidad de Málaga) by Eduardo Casilari (3333906)

“…</p><p dir="ltr">Finally, the SCRIPTS subfolder comprises two scripts written in Python and Matlab. These two programs (named Load_traces), which perform the same function, are designed to automate the downloading and processing of the data. …”

Polygon vector map distortion for increasing the readability of one-to-many flow maps: data and codes by Laetitia Viau (14057463)

“…This directory contains: </p> <p>- README file,</p> <p>- server.py: can be run from the command line to create a local server (`python3 server.py or python server.py`). This is not mandatory, it is possible to use any other solution to create a local server. …”

Landscape17 by Vlad Carare (22092515)

“…</p><p dir="ltr">We utilized TopSearch, an open-source Python package, to perform landscape exploration, at an estimated cost of 10⁵CPUh. …”