locuszoomr - Gene Locus Plot with Gene Annotations

Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots.

Last updated 30 days ago

7.04 score 19 stars 46 scripts 523 downloads

nestedcv - Nested Cross-Validation with 'glmnet' and 'caret'

Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package <doi:10.1093/bioadv/vbad048>. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) <doi:10.1111/j.2517-6161.1977.tb01603.x>. Also implemented is a method using outer CV to measure unbiased model performance metrics when fitting Bayesian linear and logistic regression shrinkage models using the horseshoe prior over parameters to encourage a sparse model as described by Piironen & Vehtari (2017) <doi:10.1214/17-EJS1337SI>.

Last updated 16 days ago

6.28 score 11 stars 41 scripts 644 downloads

glmmSeq - General Linear Mixed Models for Gene-Level Differential Expression

Using mixed effects models to analyse longitudinal gene expression can highlight differences between sample groups over time. The most widely used differential gene expression tools are unable to fit linear mixed effect models, and are less optimal for analysing longitudinal data. This package provides negative binomial and Gaussian mixed effects models to fit gene expression and other biological data across repeated samples. This is particularly useful for investigating changes in RNA-Sequencing gene expression between groups of individuals over time, as described in: Rivellese, F., Surace, A. E., Goldmann, K., Sciacca, E., Cubuk, C., Giorli, G., ... Lewis, M. J., & Pitzalis, C. (2022) Nature medicine <doi:10.1038/s41591-022-01789-0>.

Last updated 2 years ago

bioinformaticsdifferential-gene-expressiongene-expressionglmmmixed-modelstranscriptomics

5.98 score 18 stars 35 scripts 329 downloads

easylabel - Interactive Scatter Plot and Volcano Plot Labels

Interactive labelling of scatter plots, volcano plots and Manhattan plots using a 'shiny' and 'plotly' interface. Users can hover over points to see where specific points are located and click points on/off to easily label them. Labels can be dragged around the plot to place them optimally. Plots can be exported directly to PDF for publication.

Last updated 4 months ago

5.08 score 8 stars 9 scripts 282 downloads

mcprogress - Progress Bars and Messages for Parallel Processes

Tools for monitoring progress during parallel processing. Lightweight package which acts as a wrapper around mclapply() and adds a progress bar to it in 'RStudio' or 'Linux' environments. Simply replace your original call to mclapply() with pmclapply(). A progress bar can also be displayed during parallelisation via the 'foreach' package. Also included are functions to safely print messages (including error messages) from within parallelised code, which can be useful for debugging parallelised R code.

Last updated 2 months ago

4.00 score 1 stars 1 scripts 204 downloads