Package: roots 1.0
Wajid Jawaid
roots: Reconstructing Ordered Ontogenic Trajectories
A set of tools to reconstruct ordered ontogenic trajectories from single cell RNAseq data.
Authors:
roots_1.0.tar.gz
roots_1.0.tar.gz(r-4.5-noble)roots_1.0.tar.gz(r-4.4-noble)
roots_1.0.tgz(r-4.4-emscripten)roots_1.0.tgz(r-4.3-emscripten)
roots.pdf |roots.html✨
roots/json (API)
| # Install 'roots' in R: |
| install.packages('roots', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 7 years agofrom:6bd4d1fc8c. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 07 2024 |
| R-4.5-linux | OK | Dec 07 2024 |
Exports:animPlotanimPlotGifcolGraddiffuseMatdiffuseProjfastDistfindLouvainfncgetTrajgoggles
Dependencies:animationclicpp11curlglueigraphlatticelifecyclemagickmagrittrMatrixpkgconfigrARPACKRcppRcppEigenrlangRSpectravctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Animation plot | animPlot |
| Generates a GIF animating | animPlotGif |
| Apply Gaussian Kernel using Laleh Haghverdi's variable sigma | applyGaussianKernelwithVariableSigma |
| Normalise by background gene set | bgGeneNorm |
| Calculates sigmas for a distance matrix | calculateVariableSigmas |
| Generates a smooth colour gradient | colGrad |
| Generic diffusion function | diffuseMat |
| Predicts diffusion map projection from new data points | diffuseProj |
| Fast vectorised Euclidean distance calculator | fastDist |
| Filter genes | filterGenes |
| Louvain clustering on transition matrix | findLouvain |
| Find next cell function | fnc |
| Find a plausible developmental journey | getTraj |
| View single cell dataset | goggles |
| Make markov matrix sparse | sparseMarkov |