ggsci - Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'
A collection of 'ggplot2' color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.
Last updated 3 months ago
color-palettesdata-visualizationggplot2ggscisci-fiscientific-journalsvisualization
655 stars 11.02 score 28 dependencies 394 dependents
liftr - Containerize R Markdown Documents for Continuous Reproducibility
Persistent reproducible reporting by containerization of R Markdown documents.
Last updated 6 months ago
containerizationdockerdynamic-documentsknitrliftrreproducible-researchreproducible-sciencermarkdownstatistical-computing
170 stars 5.08 score 27 dependencies
protr - Generating Various Numerical Representation Schemes for Protein Sequences
Comprehensive toolkit for generating various numerical features of protein sequences described in Xiao et al. (2015) <DOI:10.1093/bioinformatics/btv042>. For full functionality, the software 'ncbi-blast+' is needed, see <https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html> for more information.
Last updated 8 days ago
bioinformaticsfeature-engineeringfeature-extractionmachine-learningpeptidesprotein-sequencessequence-analysis
52 stars 4.18 score 0 dependencies 3 dependents
hdnom - Benchmarking and Visualization Toolkit for Penalized Cox Models
Creates nomogram visualizations for penalized Cox regression models, with the support of reproducible survival model building, validation, calibration, and comparison for high-dimensional data.
Last updated 3 days ago
benchmarkhigh-dimensional-datalinear-regressionnomogram-visualizationpenalized-cox-modelssurvival-analysis
40 stars 3.65 score 40 dependencies 1 dependents
Rcpi - Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.
Last updated 8 days ago
softwaredataimportdatarepresentationfeatureextractioncheminformaticsbiomedicalinformaticsproteomicsgosystemsbiology
35 stars 3.62 score 56 dependencies
pkglite - Compact Package Representations
A tool, grammar, and standard to represent and exchange R package source code as text files. Converts one or more source packages to a text file and restores the package structures from the file.
Last updated 2 months ago
clinical-trialsectdpackaging-toolpharmaverse
30 stars 2.68 score 3 dependencies
stackgbm - Stacked Gradient Boosting Machines
A minimalist implementation of model stacking by Wolpert (1992) <doi:10.1016/S0893-6080(05)80023-1> for boosted tree models. A classic, two-layer stacking model is implemented, where the first layer generates features using gradient boosting trees, and the second layer employs a logistic regression model that uses these features as inputs. Utilities for training the base models and parameters tuning are provided, allowing users to experiment with different ensemble configurations easily. It aims to provide a simple and efficient way to combine multiple gradient boosting models to improve predictive model performance and robustness.
Last updated 4 months ago
automlcatboostdecision-treesensemble-learninggbdtgbmgradient-boostinglightgbmmachine-learningmodel-stackingxgboost
25 stars 2.32 score 14 dependencies
msaenet - Multi-Step Adaptive Estimation Methods for Sparse Regressions
Multi-step adaptive elastic-net (MSAENet) algorithm for feature selection in high-dimensional regressions proposed in Xiao and Xu (2015) <DOI:10.1080/00949655.2015.1016944>, with support for multi-step adaptive MCP-net (MSAMNet) and multi-step adaptive SCAD-net (MSASNet) methods.
Last updated 2 months ago
false-positive-controlhigh-dimensional-datalinear-regressionmachine-learningvariable-selection
13 stars 2.06 score 12 dependencies
enpls - Ensemble Partial Least Squares Regression
An algorithmic framework for measuring feature importance, outlier detection, model applicability domain evaluation, and ensemble predictive modeling with (sparse) partial least squares regressions.
Last updated 3 years ago
chemometricsdimensionality-reductionensemble-learningmachine-learningoutlier-detectionpartial-least-squares-regression
18 stars 2.06 score 79 dependencies
RECA - Relevant Component Analysis for Supervised Distance Metric Learning
Relevant Component Analysis (RCA) tries to find a linear transformation of the feature space such that the effect of irrelevant variability is reduced in the transformed space.
Last updated 5 months ago
machine-learningmetric-learning
7 stars 1.86 score 0 dependencies
OHPL - Ordered Homogeneity Pursuit Lasso for Group Variable Selection
Ordered homogeneity pursuit lasso (OHPL) algorithm for group variable selection proposed in Lin et al. (2017) <DOI:10.1016/j.chemolab.2017.07.004>. The OHPL method exploits the homogeneity structure in high-dimensional data and enjoys the grouping effect to select groups of important variables automatically. This feature makes it particularly useful for high-dimensional datasets with strongly correlated variables, such as spectroscopic data.
Last updated 2 months ago
chemometricshigh-dimensional-datahomogeneity-pursuitlassopartial-least-squares-regressionspectroscopyvariable-selection
7 stars 1.41 score 12 dependencies
grex - Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data
Convert 'Ensembl' gene identifiers from Genotype-Tissue Expression (GTEx) data to identifiers in other annotation systems, including 'Entrez', 'HGNC', and 'UniProt'.
Last updated 3 years ago
bioinformaticsgene-expressiongenotype-tissue-expressiongtex
8 stars 1.33 score 0 dependencies
ssw - Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD
Provides an R interface for 'SSW' (Striped Smith-Waterman) via its 'Python' binding 'ssw-py'. 'SSW' is a fast C/C++ implementation of the Smith-Waterman algorithm for pairwise sequence alignment using Single-Instruction-Multiple-Data (SIMD) instructions. 'SSW' enhances the standard algorithm by efficiently returning alignment information and suboptimal alignment scores. The core 'SSW' library offers performance improvements for various bioinformatics tasks, including protein database searches, short-read alignments, primary and split-read mapping, structural variant detection, and read-overlap graph generation. These features make 'SSW' particularly useful for genomic applications. Zhao et al. (2013) <doi:10.1371/journal.pone.0082138> developed the original C/C++ implementation.
Last updated 5 days ago
bioinformaticsreticulatesequence-alignmentsimdsmith-waterman
4 stars 1.24 score 12 dependencies
oneclust - Maximum Homogeneity Clustering for Univariate Data
Maximum homogeneity clustering algorithm for one-dimensional data described in W. D. Fisher (1958) <doi:10.1080/01621459.1958.10501479> via dynamic programming.
Last updated 6 months ago
clustering-algorithmfeature-engineeringhomogeneitypeak-callingunivariate-data
5 stars 1.18 score 1 dependencies