This repository contains all the functions to perform eSVD-DE (for package eSVD2, version 1.0.0 as of June 16, 2024) and the downstream analysis, for the paper “eSVD-DE: cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings”. See the companion GitHub package https://github.com/linnykos/eSVD2_examples for all the analyses performed in the paper. (Note, the original analysis was performed on eSVD2 version 0.0.0.0071, and we are working to make the code in https://github.com/linnykos/eSVD2_examples to be compatibile with the latest version of eSVD2.)

This code was developed and tested primarily on R 4.3.2. on a 2023 Macbook Pro (macOS Sonoma 14.2.1) equipped with Apple M2 Max processor (32 Gb RAM).

Tutorials and vignettes

Please see https://linnykos.github.io/eSVD2/index.html for in-depth tutorials and vignettes on how to use Tilted-CCA.

Installation

This package can be installed through devtools in R.

library("devtools")
devtools::install_github("linnykos/eSVD2")

The package itself depends on several packages. These include irlba, glmnet, locfdr, Matrix, matrixStats, Rmpfr, RSpectra, and sparseMatrixStats. See the last section of this README to see where (i.e., CRAN, Bioconductor, or GitHub) to download all such packages. We have noted that Rmpfr is sometimes tricky to install due to its required C++ libraries.

After installation of all the dependencies, the installation of the tiltedCCA package itself takes modest time (less than 10 minutes). The installation time mainly consists of time to compile the C++ code since the matrix factorization optimization was written using Rcpp for faster performance.

Known installation issues and the solutions

(Solution posted on December 24, 2023): If you come across the error,

Error in irlba::irlba() : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'

then it is likely you need to downgrade your version of Matrix to 1.6-1.1. See https://github.com/bwlewis/irlba/issues/70#issuecomment-1826900769. Hence, in the R console,

remove.packages("SeuratObject")
remove.packages("Matrix")
remove.packages("irlba")
install.packages("Matrix", type = "source")
install.packages("irlba", type = "source")
install.packages("SeuratObject")

Small simulated dataset to demo the software

See https://linnykos.github.io/eSVD2/articles/eSVD2.html for the small demo on how to use eSVD2.

Setup

The following shows the suggested package versions that the developer (GitHub username: linnykos) used when developing the eSVD2 package.

> devtools::session_info()
─ Session info ──────────────────────────
 setting  value
 version  R version 4.3.2 (2023-10-31)
 os       macOS Sonoma 14.2.1
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Chicago
 date     2024-06-16
 rstudio  2024.04.1+748 Chocolate Cosmos (desktop)
 pandoc   NA

─ Packages ──────────────────────────────
 package     * version date (UTC) lib source
 brio          1.1.5   2024-04-24 [1] CRAN (R 4.3.1)
 cachem        1.1.0   2024-05-16 [1] CRAN (R 4.3.3)
 cli           3.6.2   2023-12-11 [1] CRAN (R 4.3.1)
 devtools      2.4.5   2022-10-11 [1] CRAN (R 4.3.0)
 digest        0.6.35  2024-03-11 [1] CRAN (R 4.3.1)
 ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.3.0)
 eSVD2       * 1.0.0   2024-06-17 [1] local
 fastmap       1.2.0   2024-05-15 [1] CRAN (R 4.3.3)
 fs            1.6.4   2024-04-25 [1] CRAN (R 4.3.1)
 glue          1.7.0   2024-01-09 [1] CRAN (R 4.3.1)
 htmltools     0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1)
 htmlwidgets   1.6.4   2023-12-06 [1] CRAN (R 4.3.1)
 httpuv        1.6.15  2024-03-26 [1] CRAN (R 4.3.1)
 later         1.3.2   2023-12-06 [1] CRAN (R 4.3.1)
 lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.3.1)
 magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
 memoise       2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
 mime          0.12    2021-09-28 [1] CRAN (R 4.3.0)
 miniUI        0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
 pkgbuild      1.4.4   2024-03-17 [1] CRAN (R 4.3.1)
 pkgload       1.3.4   2024-01-16 [1] CRAN (R 4.3.1)
 profvis       0.3.8   2023-05-02 [1] CRAN (R 4.3.0)
 promises      1.3.0   2024-04-05 [1] CRAN (R 4.3.1)
 purrr         1.0.2   2023-08-10 [1] CRAN (R 4.3.0)
 R6            2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
 Rcpp        * 1.0.12  2024-01-09 [1] CRAN (R 4.3.1)
 remotes       2.5.0   2024-03-17 [1] CRAN (R 4.3.1)
 rlang         1.1.4   2024-06-04 [1] CRAN (R 4.3.3)
 rstudioapi    0.16.0  2024-03-24 [1] CRAN (R 4.3.1)
 sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
 shiny         1.8.1.1 2024-04-02 [1] CRAN (R 4.3.1)
 stringi       1.8.4   2024-05-06 [1] CRAN (R 4.3.1)
 stringr       1.5.1   2023-11-14 [1] CRAN (R 4.3.1)
 testthat    * 3.2.1.1 2024-04-14 [1] CRAN (R 4.3.1)
 urlchecker    1.0.1   2021-11-30 [1] CRAN (R 4.3.0)
 usethis       2.2.3   2024-02-19 [1] CRAN (R 4.3.1)
 vctrs         0.6.5   2023-12-01 [1] CRAN (R 4.3.1)
 xtable        1.8-4   2019-04-21 [1] CRAN (R 4.3.0)

 [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

Purpose

Tutorials and vignettes

Installation

Small simulated dataset to demo the software

Setup