Other packages > Find by keyword >

scITD  

Single-Cell Interpretable Tensor Decomposition
View on CRAN: Click here


Download and install scITD package within the R console
Install from CRAN:
install.packages("scITD")

Install from Github:
library("remotes")
install_github("cran/scITD")

Install by package version:
library("remotes")
install_version("scITD", "1.0.4")



Attach the package and use:
library("scITD")
Maintained by
Jonathan Mitchel
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-11-03
Latest Update: 2023-09-08
Description:
Single-cell Interpretable Tensor Decomposition (scITD) employs the Tucker tensor decomposition to extract multicell-type gene expression patterns that vary across donors/individuals. This tool is geared for use with single-cell RNA-sequencing datasets consisting of many source donors. The method has a wide range of potential applications, including the study of inter-individual variation at the population-level, patient sub-grouping/stratification, and the analysis of sample-level batch effects. Each "multicellular process" that is extracted consists of (A) a multi cell type gene loadings matrix and (B) a corresponding donor scores vector indicating the level at which the corresponding loadings matrix is expressed in each donor. Additional methods are implemented to aid in selecting an appropriate number of factors and to evaluate stability of the decomposition. Additional tools are provided for downstream analysis, including integration of gene set enrichment analysis and ligand-receptor analysis. Tucker, L.R. (1966) . Unkel, S., Hannachi, A., Trendafilov, N. T., & Jolliffe, I. T. (2011) . Zhou, G., & Cichocki, A. (2012) .
How to cite:
Jonathan Mitchel (2021). scITD: Single-Cell Interpretable Tensor Decomposition. R package version 1.0.4, https://cran.r-project.org/web/packages/scITD. Accessed 08 Oct. 2026.
Previous versions and publish date:
(2026-08-22 14:56), 1.0.0 (2021-11-03 21:00), 1.0.1 (2022-01-29 01:00), 1.0.2 (2022-03-23 19:20), 1.0.4 (2023-09-08 18:00)
Other packages that cited scITD R package
View scITD citation profile
Other R packages that scITD depends, imports, suggests or enhances
Complete documentation for scITD
Functions, R codes and Examples using the scITD R package
Some associated functions: apply_combat . calculate_fiber_fstats . check_rec_pres . clean_data . colMeanVars . compare_decompositions . compute_LR_interact . compute_associations . compute_donor_props . convert_gn . count_word . determine_ranks_tucker . form_tensor . get_all_lds_factor_plots . get_callouts_annot . get_ctype_exp_var . get_ctype_prop_associations . get_ctype_subc_prop_associations . get_ctype_vargenes . get_donor_meta . get_factor_exp_var . get_fstats_pvals . get_gene_modules . get_gene_set_vectors . get_indv_subtype_associations . get_intersecting_pathways . get_leading_edge_genes . get_lm_pvals . get_max_correlations . get_meta_associations . get_min_sig_genes . get_module_enr . get_normalized_variance . get_num_batch_ranks . get_one_factor . get_one_factor_gene_pvals . get_pseudobulk . get_real_fstats . get_reconstruct_errors_svd . get_significance_vectors . get_subclust_de_hmaps . get_subclust_enr_dotplot . get_subclust_enr_fig . get_subclust_enr_hmap . get_subclust_umap . get_subclusters . get_subtype_prop_associations . get_sums . ht_clusters . identify_sex_metadata . initialize_params . instantiate_scMinimal . is_GO_id . make_new_container . merge_small_clusts . nmf_unfolded . norm_var_helper . normalize_counts . normalize_pseudobulk . parse_data_by_ctypes . pca_unfolded . plotDEheatmap_conos . plot_donor_matrix . plot_donor_props . plot_donor_sig_genes . plot_dscore_enr . plot_gsea_hmap . plot_gsea_hmap_w_similarity . plot_gsea_sub . plot_loadings_annot . plot_mod_and_lig . plot_multi_module_enr . plot_rec_errors_bar_svd . plot_rec_errors_line_svd . plot_scores_by_meta . plot_select_sets . plot_stability_results . plot_subclust_associations . prep_LR_interact . project_new_data . reduce_dimensions . reduce_to_vargenes . render_multi_plots . reshape_loadings . run_fgsea . run_gsea_one_factor . run_hypergeometric_gsea . run_jackstraw . run_stability_analysis . run_tucker_ica . sample_fibers . scale_fontsize . scale_variance . seurat_to_scMinimal . shuffle_fibers . stack_tensor . stop_wrap . subset_scMinimal . test_container . tucker_ica_helper . update_params . vargenes_anova . 
Some associated R codes: RcppExports.R . convert_gn.R . data.R . determine_ranks_tucker.R . form_tensor.R . get_LR_interact.R . get_meta_associations.R . get_prop_associations.R . manage_container.R . manage_scMinimal.R . plot_tucker.R . run_gsea.R . run_jackstraw.R . run_tucker_ica.R . test_stability.R .  Full scITD package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

abc.data  
Data Only: Tools for Approximate Bayesian Computation (ABC)
Contains data which are used by functions of the 'abc' package. ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
climwin  
Climate Window Analysis
Contains functions to detect and visualise periods of climate sensitivity (climate windows) for a g ...
Download / Learn more Package Citations See dependency  
metafor  
Meta-Analysis Package for R
A comprehensive collection of functions for conducting meta-analyses in R. The package includes func ...
Download / Learn more Package Citations See dependency  
dineR  
Differential Network Estimation in R
An efficient and convenient set of functions to perform differential network estimation through the ...
Download / Learn more Package Citations See dependency  
colorfindr  
Extract Colors from Windows BMP, JPEG, PNG, TIFF, and SVG Format Images
Extracts colors from various image types, returns customized reports and plots treemaps and 3D scat ...
Download / Learn more Package Citations See dependency  

28,905

R Packages

247,686

Dependencies

76,495

Author Associations

28,906

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA