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stephenslab / fastTopics

Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.
https://stephenslab.github.io/fastTopics
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count not find function "diff_count_clusters" #24

Closed guanxn90 closed 2 years ago

guanxn90 commented 2 years ago

Thanks a lot for developing this great package.

I installed the 'fastTopics' through remotes::install_github("stephenslab/fastTopics"), I am following the tutorial, but at interpreting topics by analyzing gene expression differences error occurs saying cannot find the diff_count_cluster function.

Thanks a lot, Guan

R4.0.2 and sessionInfo: attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] Matrix_1.3-2 patchwork_1.1.0 cowplot_1.1.0 ggplot2_3.3.2 rstudioapi_0.12 fastTopics_0.6-98

loaded via a namespace (and not attached): [1] ggrepel_0.9.1 Rcpp_1.0.5 invgamma_1.1 lattice_0.20-41 tidyr_1.1.2 prettyunits_1.1.1 digest_0.6.27
[8] truncnorm_1.0-8 R6_2.5.0 MatrixModels_0.4-1 coda_0.19-4 httr_1.4.2 pillar_1.4.6 rlang_0.4.11
[15] progress_1.2.2 lazyeval_0.2.2 data.table_1.14.2 irlba_2.3.3 SparseM_1.78 labeling_0.4.2 Rtsne_0.15
[22] htmlwidgets_1.5.2 munsell_0.5.0 uwot_0.1.8 mixsqp_0.3-43 tinytex_0.27 compiler_4.0.2 xfun_0.19
[29] pkgconfig_2.0.3 SQUAREM_2020.5 mcmc_0.9-7 htmltools_0.5.1.1 tidyselect_1.1.0 tibble_3.0.4 quadprog_1.5-8
[36] matrixStats_0.57.0 viridisLite_0.3.0 crayon_1.3.4 dplyr_1.0.2 conquer_1.0.2 withr_2.3.0 MASS_7.3-53
[43] grid_4.0.2 jsonlite_1.7.1 gtable_0.3.0 lifecycle_0.2.0 magrittr_1.5 scales_1.1.1 RcppParallel_5.0.2 [50] pbapply_1.4-3 farver_2.0.3 ellipsis_0.3.1 generics_0.1.0 vctrs_0.3.4 tools_4.0.2 glue_1.4.2
[57] purrr_0.3.4 hms_0.5.3 parallel_4.0.2 colorspace_1.4-1 ashr_2.2-54 plotly_4.9.2.1 quantreg_5.86
[64] MCMCpack_1.5-0

fastTopics extends

pcarbo commented 2 years ago

@guanxn90 Please use de_analysis instead; these are newly developed methods and they haven't been fully documented. If you have questions about de_analysis please post here.

guanxn90 commented 2 years ago

@pcarbo Thanks a lot for quick response. The de_analysis works and the help ?de_analysis is clear.