Hello

Firstly, I'd like to thank you for publishing the valuable scRNA seq dataset.

Could you give me advice on identifying the name of cell-types from the Rdata file?

I can see that load("data/HumanLiver/inst/liver/HumanLiver.RData") loads two variables, HumanLiverSeurat and sCVdL, into workspace.

And I found gene-cell matrix is in HumanLiverSeurat[['RNA']]@data( in case of raw count, HumanLiverSeurat[['RNA']]@counts)

I guess that cluster(or cell type) information is in [email protected](or [email protected]$res.0.8, which is the same as it) as the number of unique values is 20, which is in line with that of publication.
However, I failed to identify to which cell-types each integer in active.ident column corresponds.
(ex.endothelial cells, cholangiocytes, hepatic stellate cells, B cells, etc.)

Could you help me out with this? Am I missing something?
Thank you for your help in advance,

Best regards,
Chanwoo Kim

Dear all,

I am having issues to install the "HumanLiver" package.
I am running the newest version of R (4.0.0) on MacOS and all the packages are also updated.

`> devtools::install_github("BaderLab/HumanLiver")
Downloading GitHub repo BaderLab/HumanLiver@master
✓ checking for file ‘/private/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T/Rtmp3cE6pF/remotes10e17b3a97b/BaderLab-HumanLiver-39c873b/DESCRIPTION’ ...
─ preparing ‘HumanLiver’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: ‘HumanLiver/inst/liver/HumanLiver.RData’
─ building ‘HumanLiver_1.5.0.tar.gz’

• installing source package ‘HumanLiver’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  sh: line 1: 4621 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T//RtmpcNy9lM/file120675b2df47'
  ERROR: lazy loading failed for package ‘HumanLiver’
• removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/HumanLiver’
  installation of package ‘/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T//Rtmp3cE6pF/file10e1243bce30/HumanLiver_1.5.0.tar.gz’ had non-zero exit status`

As you can see the installation fails and I am not sure why. Do you have an idea what the problem could be?

Thank you.
Best regards,
E. Viho

Hello,

I recently updated my R packages, in particular the scClustViz from v0.5.2 (I think) to v1.0.0. Now after loading the HumanLiver package and running viewHumanLiver(), I get the following error:

Error in FUN(X[[i]], ...) : Unexpected input object.
In addition: Warning messages:
1: replacing previous import ‘BiocGenerics::dims’ by ‘Biobase::dims’ when loading ‘AnnotationDbi’
2: In if (is(get(lfc[X])[[1]]) == "sCVdata") { :
the condition has length > 1 and only the first element will be used

Any idea what could cause this?

Thank you for your help in advance,
Juliane

My sessionInfo output:

R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] Matrix_1.2-8 org.Hs.eg.db_3.7.0 AnnotationDbi_1.44.0 IRanges_2.16.0
[5] S4Vectors_0.20.1 Biobase_2.40.0 BiocGenerics_0.28.0 HumanLiver_1.2.0

loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 remotes_2.0.2 purrr_0.3.0 lattice_0.20-34 colorspace_1.4-0
[6] testthat_1.0.2 viridisLite_0.3.0 usethis_1.4.0 htmltools_0.3.6 blob_1.1.1
[11] rlang_0.3.1 pkgbuild_1.0.2 pillar_1.3.1 later_0.8.0 glue_1.3.0
[16] withr_2.1.2 DBI_1.0.0 bit64_0.9-5 bindrcpp_0.2.2 sessioninfo_1.1.1
[21] bindr_0.1.1 plyr_1.8.4 munsell_0.5.0 gtable_0.2.0 devtools_2.0.1
[26] memoise_1.0.0 callr_3.1.1 httpuv_1.4.5.1 ps_1.3.0 curl_3.3
[31] Rcpp_1.0.0 xtable_1.8-3 backports_1.1.3 promises_1.0.1 scales_1.0.0
[36] desc_1.2.0 pkgload_1.0.2 mime_0.6 fs_1.2.6 bit_1.1-14
[41] gridExtra_2.3 ggplot2_3.1.0 digest_0.6.18 dplyr_0.7.8 processx_3.2.1
[46] shiny_1.2.0 rprojroot_1.2 grid_3.5.0 cli_1.0.1 tools_3.5.0
[51] magrittr_1.5 tibble_2.0.1 lazyeval_0.2.1 RSQLite_2.1.1 crayon_1.3.4
[56] pkgconfig_2.0.2 scClustViz_1.0.0 prettyunits_1.0.2 assertthat_0.2.0 rstudioapi_0.9.0
[61] viridis_0.5.1 R6_2.4.0 compiler_3.5.0

Hi,
I want to know the unit of the data you provided in HuamanLiverSeurat@data so I can run some downstream analysis of my own. Is it log2(TPM + 1) and is it scaled somehow?
Thx.