bioturing / signac Goto Github PK

Hello,

I am trying to run VeniceFindMarkers on a Seurat v3.1.5 integrated object with the default assay as SCT. Below is the line I'm trying to run.

VeniceFindMarkers(object = integrated, assay = "SCT", ident.1 = patient.neur.1, ident.2 = control.neur.1, logfc.threshold = 0)

The above line gives me the following error.

Error in as.character(x = ide5nt.2) %in% colnames(x = data.use) : object 'ide5nt.2' not found

TRACEBACK:

3. as.character(x = iden5nt.2) %in% colnames(x = data.use)
2. GetCellsIndices(data.use, object, ident.1, ident.2)
1. VeniceFindMarkers(object = integrated, assay = "SCT", ident.1 = patient.neur.1, ident.2 = control.neur.1, logfc.threshold = 0)

Can you please suggest a solution?
Thank you

Is it possible to control for covariates/latent variables (categorical and continuous variables) during DE?

CoveragePlot(
object = pbmc,
region = rownames(da_peaks)[c(1,5)],
sep = c(":", "-"),
annotation = EnsDb.Hsapiens.v75,
extend.upstream = 20000,
extend.downstream = 20000,
ncol = 1
)
This function has error when I tested the tutorial of signac. Could you please help me address this issue?

• S3 object
• Follow Seurat object
• Add some unique features of BioTuring

Hi,

I was trying to install your package but got the following error message. Is there a fix for that? Thanks!

Lei

R> devtools::install_github("bioturing/signac")
......
Error : (converted from warning) /private/var/folders/k0/9pl_mjpn6wd669_r6z7r93_h0000gp/T/RtmpMW7T6d/R.INSTALL1180b5babfd66/Signac/man/Colourise.Rd:28: unexpected macro '\dontrun'
ERROR: installing Rd objects failed for package ‘Signac’

• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Signac’
  Error: Failed to install 'Signac' from GitHub:
  (converted from warning) installation of package ‘/var/folders/k0/9pl_mjpn6wd669_r6z7r93_h0000gp/T//Rtmp3w9Rgp/filed56a69c6e6e6/Signac_0.0.0.9000.tar.gz’ had non-zero exit status

R> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 ps_1.3.0 prettyunits_1.0.2 rprojroot_1.3-2
[5] digest_0.6.20 crayon_1.3.4 withr_2.1.2 assertthat_0.2.1
[9] R6_2.4.0 backports_1.1.4 git2r_0.26.1 magrittr_1.5
[13] rlang_0.4.0 cli_1.1.0 curl_3.3 fs_1.3.1
[17] remotes_2.1.0 testthat_2.1.1 callr_3.3.0 devtools_2.1.0
[21] desc_1.2.0 tools_3.6.1 glue_1.3.1 pkgload_1.0.2
[25] compiler_3.6.1 processx_3.4.0 pkgbuild_1.0.3 sessioninfo_1.1.1
[29] memoise_1.1.0.9000 usethis_1.5.1

Hello,

I am trying to find the marker genes of a certain cluster with respect to all other clusters in my Seurat v3 object. In order to do this, I would have to set the only.pos parameter to TRUE or else I would get also markers of the rest of the clusters. However, when I do this, I still see negative logfc values.

Thank you

Hi, thanks for the very interesting package, I wanted to try it but when installing with devtools i get a bunch of warnings at the compilation stage. the last one is this

clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Signac.so CommonUtil.o Hdf5Util.o MatrixUtil.o RcppExports.o SparseMatrixUtil.o Venice.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm /Users/fc7/Library/R/4.0/library/Rhdf5lib/lib/libhdf5_cpp.a /Users/fc7/Library/R/4.0/library/Rhdf5lib/lib/libhdf5.a /Users/fc7/Library/R/4.0/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [Signac.so] Error 1
ERROR: compilation failed for package ‘Signac’
* removing ‘/Users/fc7/Library/R/4.0/library/Signac’
Warning message:
In i.p(...) : 
installation of package ‘/var/folders/6f/r101x9pj4bj3grn96jv0725h000m5j/T//RtmpnOqaCZ/file16b7573eaa188/Signac_0.0.9.tar.gz’ had non-zero exit status 

my gfrortran and clang are:

$ gfortran --version
GNU Fortran (Homebrew GCC 10.2.0_4) 10.2.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ clang --version
Apple clang version 12.0.0 (clang-1200.0.32.29)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

any help much appreciated!
thanks!