Package: switchde 1.33.0

Kieran Campbell

switchde: Switch-like differential expression across single-cell trajectories

Inference and detection of switch-like differential expression across single-cell RNA-seq trajectories.

Authors:Kieran Campbell [aut, cre]

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switchde.pdf |switchde.html✨
switchde/json (API)
NEWS

# Install 'switchde' in R:

install.packages('switchde', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kieranrcampbell/switchde/issues

Datasets:

ex_pseudotime - Synthetic gene pseudotimes
synth_gex - Synthetic gene expression matrix

On BioConductor:switchde-1.33.0(bioc 3.21)switchde-1.32.0(bioc 3.20)

immunooncology software transcriptomics geneexpression rnaseq regression differentialexpression singlecell gene-expression genomics single-cell

5.98 score 19 stars 6 scripts 185 downloads 5 mentions 6 exports 57 dependencies

Last updated 23 days agofrom:bf3d5a31bc. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 18 2024
R-4.5-win	WARNING	Nov 18 2024
R-4.5-linux	WARNING	Nov 18 2024
R-4.4-win	WARNING	Nov 18 2024
R-4.4-mac	WARNING	Nov 18 2024
R-4.3-win	WARNING	Nov 18 2024
R-4.3-mac	WARNING	Nov 18 2024

Exports:example_sigmoid extract_pars fit_nzi_model fit_zi_model switchde switchplot

Dependencies:abind askpass Biobase BiocGenerics cli colorspace crayon curl DelayedArray dplyr fansi farver generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig R6 RColorBrewer rlang S4Arrays S4Vectors scales SingleCellExperiment SparseArray SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

switchde: inference of switch-like gene behaviour along single-cell trajectories

Kieran Campbell

Rendered fromswitchde_vignette.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2018-08-30
Started: 2016-07-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Synthetic gene pseudotimes	ex_pseudotime
Example sigmoid plot	example_sigmoid
Extract parameters from fitted model	extract_pars
Fit a (non-zero-inflated) model for a single gene	fit_nzi_model
Fit a zero-inflated model for a single gene	fit_zi_model
Switch-like model fitting and differential expression test	switchde
Plot gene behaviour	switchplot
Synthetic gene expression matrix	synth_gex

Usage by other packages (reverse dependencies)