Ah, looks like I can't even procrastinate on StackExchange anymore without seeing work-related stuff. Oh well.
Anyway, the other answers and comments are way off. scran has supported sparse matrices for years, ever since we switched over to the
SingleCellExperiment class as our basic data structure.
quickCluster does no coercion to dense format unless you tell it so explicitly, e.g., with
use.ranks=TRUE (in which case you're asking for ranks, so there's little choice but to collapse to a dense matrix).
You don't provide an MWE or your session information, but this is how it rolls for me:
# Using the raw counts in the linked dataset. Despite being
# called a CSV, it's actually space delimited... typical.
mat <- readSparseCounts("GBM_raw_gene_counts.csv", sep=" ")
# Making an SCE just for fun. Not strictly necessary for
# this example, but you'll find it useful later.
sce <- SingleCellExperiment(list(counts=mat))
system.time(clust <- quickCluster(sce))
## user system elapsed
## 3.170 0.174 3.411
This is running on my laptop - 16 GB RAM but I'm definitely not using all of it. I only go full throttle when I'm working on some real data, e.g., the 300k HCA bone marrow dataset. Check out the book for more details.
Session info below, I don't know quite enough SO-fu to know collapse it.
R version 4.0.0 Patched (2020-04-27 r78316)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
attached base packages:
 parallel stats4 stats graphics grDevices utils datasets
 methods base
other attached packages:
 scran_1.16.0 scater_1.16.1
 ggplot2_3.3.2 SingleCellExperiment_1.10.1
 SummarizedExperiment_1.18.1 DelayedArray_0.14.0
 matrixStats_0.56.0 Biobase_2.48.0
 GenomicRanges_1.40.0 GenomeInfoDb_1.24.2
 IRanges_2.22.2 S4Vectors_0.26.1
loaded via a namespace (and not attached):
 beeswarm_0.2.3 statmod_1.4.34
 tidyselect_1.1.0 locfit_1.5-9.4
 purrr_0.3.4 BiocSingular_1.4.0
 lattice_0.20-41 colorspace_1.4-1
 vctrs_0.3.1 generics_0.0.2
 viridisLite_0.3.0 rlang_0.4.6
 pillar_1.4.4 glue_1.4.1
 withr_2.2.0 BiocParallel_1.22.0
 dqrng_0.2.1 GenomeInfoDbData_1.2.3
 lifecycle_0.2.0 zlibbioc_1.34.0
 munsell_0.5.0 gtable_0.3.0
 rsvd_1.0.3 vipor_0.4.5
 irlba_2.3.3 BiocNeighbors_1.6.0
 Rcpp_220.127.116.11 edgeR_3.30.3
 scales_1.1.1 limma_3.44.3
 XVector_0.28.0 gridExtra_2.3
 dplyr_1.0.0 grid_4.0.0
 tools_4.0.0 bitops_1.0-6
 magrittr_1.5 RCurl_1.98-1.2
 tibble_3.0.1 crayon_1.3.4
 pkgconfig_2.0.3 ellipsis_0.3.1
 Matrix_1.2-18 DelayedMatrixStats_1.10.0
 ggbeeswarm_0.6.0 viridis_0.5.1
 R6_2.4.1 igraph_1.2.5