Overview | Section 1 - Preliminaries | 1-1 Load SparseMDC | 1-2 Real Data Example:Biase Data | 1-3 Data Formatting | Section 2 - Preprocessing | Section 3 - Penalty Parameter Estimation | 3-1 $\lambda_{1}$ | 3-2 $\lambda_{2}$ | Section 4 - SparseMDC | 4-1 Apply SparseMDC | 4-2 Examine Results | 4-3 Housekeeping Marker Genes | 4-4 Condition-Dependent/Condition-Specific Marker Genes | References
Package: SparseMDC 0.99.5
SparseMDC: Implementation of SparseMDC Algorithm
Implements the algorithm described in Barron, M., and Li, J. (Not yet published). This algorithm clusters samples from multiple ordered populations, links the clusters across the conditions and identifies marker genes for these changes. The package was designed for scRNA-Seq data but is also applicable to many other data types, just replace cells with samples and genes with variables. The package also contains functions for estimating the parameters for SparseMDC as outlined in the paper. We recommend that users further select their marker genes using the magnitude of the cluster centers.
Authors:
SparseMDC_0.99.5.tar.gz
SparseMDC_0.99.5.zip(r-4.7-any)SparseMDC_0.99.5.zip(r-4.6-any)SparseMDC_0.99.5.zip(r-4.5-any)
SparseMDC_0.99.5.tgz(r-4.6-any)SparseMDC_0.99.5.tgz(r-4.5-any)
SparseMDC_0.99.5.tar.gz(r-4.7-any)SparseMDC_0.99.5.tar.gz(r-4.6-any)
SparseMDC_0.99.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SparseMDC/json (API)
| # Install 'SparseMDC' in R: |
| install.packages('SparseMDC', repos = c('https://jli-stat.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- cell_type_biase - Biase Data Cell Type
- condition_biase - Biase Data Conditions
- data_biase - Biase Data
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:d7f74c8548. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 123 | ||
| source / vignettes | OK | 186 | ||
| linux-release-x86_64 | NOTE | 101 | ||
| macos-release-arm64 | NOTE | 126 | ||
| macos-oldrel-arm64 | NOTE | 186 | ||
| windows-devel | NOTE | 91 | ||
| windows-release | NOTE | 70 | ||
| windows-oldrel | NOTE | 84 | ||
| wasm-release | OK | 97 |
Exports:lambda1_calculatorlambda2_calculatormu_calcmu_solverpen_calculatorpre_proc_dataS_funcscore_calcsdc_mparsparse_mdcsparsemdc_gapupdate_cupdate_mu
Dependencies:codetoolsdigestdoParalleldoRNGforeachiteratorsrngtools
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Biase Data Cell Type | cell_type_biase |
| Biase Data Conditions | condition_biase |
| Biase Data | data_biase |
| Uniform data generator For use with the gap statistic. Generates datasets drawn from the reference distribution where each reference feature is generated uniformly over the range of observed values for that feature. | generate_uni_dat |
| Lambda 1 Calcualtor | lambda1_calculator |
| Lambda 2 Calculator | lambda2_calculator |
| mu Calculator | mu_calc |
| Mu Solver | mu_solver |
| Penalty calculator | pen_calculator |
| Pre-process data | pre_proc_data |
| The soft thresholding operator | S_func |
| Score calculator | score_calc |
| SparseDC Multi Parallel | sdc_mpar |
| SparseDC Multi | sparse_mdc |
| Gap Statistic Calculator | sparsemdc_gap |
| update_c | update_c |
| update_mu | update_mu |
