Package: scTenifoldNet 1.4
Daniel Osorio
scTenifoldNet: Construct and Compare scGRN from Single-Cell Transcriptomic Data
A workflow based on machine learning methods to construct and compare single-cell gene regulatory networks (scGRN) using single-cell RNA-seq (scRNA-seq) data collected from different conditions. Uses principal component regression, tensor decomposition, and manifold alignment, to accurately identify even subtly shifted gene expression programs. See <doi:10.1016/j.patter.2020.100139> for more details.
Authors:
scTenifoldNet_1.4.tar.gz
scTenifoldNet_1.4.zip(r-4.7)scTenifoldNet_1.4.zip(r-4.6)scTenifoldNet_1.4.zip(r-4.5)
scTenifoldNet_1.4.tgz(r-4.6-x86_64)scTenifoldNet_1.4.tgz(r-4.6-arm64)scTenifoldNet_1.4.tgz(r-4.5-x86_64)scTenifoldNet_1.4.tgz(r-4.5-arm64)
scTenifoldNet_1.4.tar.gz(r-4.7-arm64)scTenifoldNet_1.4.tar.gz(r-4.7-x86_64)scTenifoldNet_1.4.tar.gz(r-4.6-arm64)scTenifoldNet_1.4.tar.gz(r-4.6-x86_64)
scTenifoldNet_1.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scTenifoldNet/json (API)
| # Install 'scTenifoldNet' in R: |
| install.packages('scTenifoldNet', repos = c('https://cailab-tamu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cailab-tamu/sctenifoldnet/issues
differential-regulation-analysisgene-regulatory-networksmanifold-alignmentsingle-celltensor-decompositionopenblascpp
Last updated from:d7505cf962. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 143 | ||
| linux-devel-x86_64 | OK | 197 | ||
| source / vignettes | OK | 191 | ||
| linux-release-arm64 | OK | 137 | ||
| linux-release-x86_64 | OK | 141 | ||
| macos-release-arm64 | OK | 138 | ||
| macos-release-x86_64 | OK | 298 | ||
| macos-oldrel-arm64 | OK | 120 | ||
| macos-oldrel-x86_64 | OK | 226 | ||
| windows-devel | OK | 164 | ||
| windows-release | OK | 141 | ||
| windows-oldrel | OK | 182 | ||
| wasm-release | OK | 125 |
Exports:cpmNormalizationdRegulationmakeNetworksmanifoldAlignmentpcNetscQCscTenifoldNettensorDecomposition
Dependencies:clicodetoolsdigestfurrrfutureglobalsgluelatticelifecyclelistenvmagrittrMASSMatrixparallellypurrrRcppRcppArmadilloRcppEigenRhpcBLASctlrlangRSpectravctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Canonical Polyadic Decomposition | cpDecomposition |
| Performs counts per million (CPM) data normalization | cpmNormalization |
| Evaluates gene differential regulation based on manifold alignment distances. | dRegulation |
| Computes gene regulatory networks for subsamples of cells based on principal component regression. | makeNetworks |
| Performs non-linear manifold alignment of two gene regulatory networks. | manifoldAlignment |
| Principal Component Network Analysis | pcNet |
| Performs single-cell data quality control | scQC |
| scTenifoldNet | scTenifoldNet |
| Performs CANDECOMP/PARAFAC (CP) Tensor Decomposition. | tensorDecomposition |