Showing 12 of total 12 results (show query)
wilkelab
cowplot:Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.
Maintained by Claus O. Wilke. Last updated 3 months ago.
714 stars 18.83 score 75k scripts 1.4k dependents
privefl
bigstatsr:Statistical Tools for Filebacked Big Matrices
Easy-to-use, efficient, flexible and scalable statistical tools. Package bigstatsr provides and uses Filebacked Big Matrices via memory-mapping. It provides for instance matrix operations, Principal Component Analysis, sparse linear supervised models, utility functions and more <doi:10.1093/bioinformatics/bty185>.
Maintained by Florian Privé. Last updated 7 months ago.
big-datalarge-matricesmemory-mapped-fileparallel-computingstatistical-methodsopenblascppopenmp
180 stars 10.59 score 394 scripts 16 dependents
ramikrispin
TSstudio:Functions for Time Series Analysis and Forecasting
Provides a set of tools for descriptive and predictive analysis of time series data. That includes functions for interactive visualization of time series objects and as well utility functions for automation time series forecasting.
Maintained by Rami Krispin. Last updated 2 years ago.
forecastingtime-seriestimeseriestsstudiovisualization
425 stars 9.02 score 656 scripts
masurp
specr:Conducting and Visualizing Specification Curve Analyses
Provides utilities for conducting specification curve analyses (Simonsohn, Simmons & Nelson (2020, <doi: 10.1038/s41562-020-0912-z>) or multiverse analyses (Steegen, Tuerlinckx, Gelman & Vanpaemel, 2016, <doi: 10.1177/1745691616658637>) including functions to setup, run, evaluate, and plot all specifications.
Maintained by Philipp K. Masur. Last updated 10 months ago.
68 stars 7.89 score 85 scripts
bioc
scMultiSim:Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell Interactions
scMultiSim simulates paired single cell RNA-seq, single cell ATAC-seq and RNA velocity data, while incorporating mechanisms of gene regulatory networks, chromatin accessibility and cell-cell interactions. It allows users to tune various parameters controlling the amount of each biological factor, variation of gene-expression levels, the influence of chromatin accessibility on RNA sequence data, and so on. It can be used to benchmark various computational methods for single cell multi-omics data, and to assist in experimental design of wet-lab experiments.
Maintained by Hechen Li. Last updated 5 months ago.
singlecelltranscriptomicsgeneexpressionsequencingexperimentaldesign
23 stars 7.08 score 11 scripts
paulregular
SimSurvey:Test Surveys by Simulating Spatially-Correlated Populations
Simulate age-structured populations that vary in space and time and explore the efficacy of a range of built-in or user-defined sampling protocols to reproduce the population parameters of the known population. (See Regular et al. (2020) <doi:10.1371/journal.pone.0232822> for more details).
Maintained by Paul Regular. Last updated 2 months ago.
analysisfisheries-researchsimulation-testingsurvey-design
12 stars 6.28 score 106 scripts
centerforstatistics-ugent
xnet:Two-Step Kernel Ridge Regression for Network Predictions
Fit a two-step kernel ridge regression model for predicting edges in networks, and carry out cross-validation using shortcuts for swift and accurate performance assessment (Stock et al, 2018 <doi:10.1093/bib/bby095> ).
Maintained by Joris Meys. Last updated 4 years ago.
11 stars 5.30 score 12 scripts
moritzpschwarz
getspanel:General-to-Specific Modelling of Panel Data
Uses several types of indicator saturation and automated General-to-Specific (GETS) modelling from the 'gets' package and applies it to panel data. This allows the detection of structural breaks in panel data, operationalising a reverse causal approach of causal inference, see Pretis and Schwarz (2022) <doi:10.2139/ssrn.4022745>.
Maintained by Moritz Schwarz. Last updated 2 days ago.
13 stars 5.19 score 24 scripts
alphaprime7
normfluodbf:Cleans and Normalizes FLUOstar DBF and DAT Files from 'Liposome' Flux Assays
Cleans and Normalizes FLUOstar DBF and DAT Files obtained from liposome flux assays. Users should verify extended usage of the package on files from other assay types.
Maintained by Tingwei Adeck. Last updated 5 months ago.
1 stars 4.98 score 12 scripts
epiforecasts
EpiNow:Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
To identify changes in the reproduction number, rate of spread, and doubling time during the course of outbreaks whilst accounting for potential biases due to delays in case reporting.
Maintained by Sam Abbott. Last updated 5 years ago.
33 stars 4.74 score 111 scripts
mkborregaard
nodiv:Compares the Distribution of Sister Clades Through a Phylogeny
An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped.
Maintained by Michael Krabbe Borregaard. Last updated 2 years ago.
2 stars 3.45 score 28 scripts
