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 7 months ago

color-palettesdata-visualizationggplot2ggscisci-fiscientific-journalsvisualization

17.83 score 676 stars 414 dependents 25k scripts 99k downloads

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 4 months ago

bioinformaticsfeature-engineeringfeature-extractionmachine-learningpeptidesprotein-sequencessequence-analysis

9.99 score 52 stars 3 dependents 173 scripts 613 downloads

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 5 months ago

benchmarkhigh-dimensional-datalinear-regressionnomogram-visualizationpenalized-cox-modelssurvival-analysisopenblas

8.20 score 43 stars 1 dependents 68 scripts 407 downloads

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 3 months ago

softwaredataimportdatarepresentationfeatureextractioncheminformaticsbiomedicalinformaticsproteomicsgosystemsbiologybioconductorbioinformaticsdrug-discoveryfeature-extractionfingerprintmolecular-descriptorsprotein-sequences

7.81 score 37 stars 29 scripts 323 downloads

liftr - Containerize R Markdown Documents for Continuous Reproducibility

Persistent reproducible reporting by containerization of R Markdown documents.

Last updated 11 months ago

containerizationdockerdynamic-documentsknitrliftrreproducible-researchreproducible-sciencermarkdownstatistical-computing

7.03 score 172 stars 21 scripts 304 downloads

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

6.94 score 30 stars 12 scripts 753 downloads

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 6 months ago

false-positive-controlhigh-dimensional-datalinear-regressionmachine-learningvariable-selection

6.23 score 13 stars 52 scripts 346 downloads

gMCPLite - Lightweight Graph Based Multiple Comparison Procedures

A lightweight fork of 'gMCP' with functions for graphical described multiple test procedures introduced in Bretz et al. (2009) <doi:10.1002/sim.3495> and Bretz et al. (2011) <doi:10.1002/bimj.201000239>. Implements a flexible function using 'ggplot2' to create multiplicity graph visualizations. Contains instructions of multiplicity graph and graphical testing for group sequential design, described in Maurer and Bretz (2013) <doi:10.1080/19466315.2013.807748>, with necessary unit testing using 'testthat'.

Last updated 11 months ago

6.05 score 10 stars 14 scripts 244 downloads

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

5.56 score 18 stars 40 scripts 289 downloads

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 9 months ago

automlcatboostdecision-treesensemble-learninggbdtgbmgradient-boostinglightgbmmachine-learningmodel-stackingxgboost

5.40 score 25 stars 3 scripts 483 downloads

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' and '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' and 'C++' implementation.

Last updated 4 months ago

bioinformaticsreticulatesequence-alignmentsimdsmith-waterman

5.10 score 5 stars 382 downloads

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

4.96 score 8 stars 23 scripts 294 downloads

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 11 months ago

clustering-algorithmfeature-engineeringhomogeneitypeak-callingunivariate-datacpp

4.40 score 5 stars 149 downloads

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 9 months ago

machine-learningmetric-learning

4.02 score 7 stars 4 scripts 137 downloads

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 6 months ago

chemometricshigh-dimensional-datahomogeneity-pursuitlassopartial-least-squares-regressionspectroscopyvariable-selection

3.85 score 7 stars 9 scripts 137 downloads