Package: phateR 1.0.7
phateR: PHATE - Potential of Heat-Diffusion for Affinity-Based Transition Embedding
PHATE is a tool for visualizing high dimensional single-cell data with natural progressions or trajectories. PHATE uses a novel conceptual framework for learning and visualizing the manifold inherent to biological systems in which smooth transitions mark the progressions of cells from one state to another. To see how PHATE can be applied to single-cell RNA-seq datasets from hematopoietic stem cells, human embryonic stem cells, and bone marrow samples, check out our publication in Nature Biotechnology at <doi:10.1038/s41587-019-0336-3>.
Authors:
phateR_1.0.7.tar.gz
phateR_1.0.7.zip(r-4.5)phateR_1.0.7.zip(r-4.4)phateR_1.0.7.zip(r-4.3)
phateR_1.0.7.tgz(r-4.4-any)phateR_1.0.7.tgz(r-4.3-any)
phateR_1.0.7.tar.gz(r-4.5-noble)phateR_1.0.7.tar.gz(r-4.4-noble)
phateR_1.0.7.tgz(r-4.4-emscripten)phateR_1.0.7.tgz(r-4.3-emscripten)
phateR.pdf |phateR.html✨
phateR/json (API)
| # Install 'phateR' in R: |
| install.packages('phateR', repos = c('https://scottgigante.r-universe.dev', 'https://cloud.r-project.org')) |
- tree.data - Fake branching data for examples
- tree.data.small - Fake branching data for running examples fast
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 4 years agofrom:e0cd10e1ed. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 15 2024 |
| R-4.5-win | OK | Nov 15 2024 |
| R-4.5-linux | OK | Nov 15 2024 |
| R-4.4-win | OK | Nov 15 2024 |
| R-4.4-mac | OK | Nov 15 2024 |
| R-4.3-win | OK | Nov 15 2024 |
| R-4.3-mac | OK | Nov 15 2024 |
Exports:check_pyphate_versioncluster_phateinstall.phatelibrary.size.normalizephate
Dependencies:cachemclicolorspacefansifarverfastmapggplot2gluegtablehereisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmunsellnlmepillarpkgconfigpngR6rappdirsRColorBrewerRcppRcppTOMLreticulaterlangrprojrootscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert a PHATE object to a data.frame | as.data.frame.phate |
| Convert a PHATE object to a matrix | as.matrix.phate |
| Check that the current PHATE version in Python is up to date. | check_pyphate_version |
| KMeans on the PHATE potential Clustering on the PHATE operator as introduced in Moon et al. This is similar to spectral clustering. | cluster_phate |
| Convert a PHATE object to a data.frame for ggplot | ggplot.phate |
| Install PHATE Python Package | install.phate |
| Performs L1 normalization on input data such that the sum of expression values for each cell sums to 1, then returns normalized matrix to the metric space using median UMI count per cell effectively scaling all cells as if they were sampled evenly. | library.size.normalize |
| Run PHATE on an input data matrix | phate |
| Plot a PHATE object in base R | plot.phate |
| Print a PHATE object | print.phate |
| Summarize a PHATE object | summary.phate |
| Fake branching data for examples | tree.data |
| Fake branching data for running examples fast | tree.data.small |
