jiang-junyao / irena Goto Github PK

Hi,
This may be a naive question - Is the pseudotime information absolutely required for IReNA analysis? I'm interested in inferring cell-type-specific regulatory networks from a heterogeneous population (e.g. tumor microenvironment). I do not expect one cell type will progress to another cell type, so it doesn't make sense to me to reconstruct the trajectory. Would you please give me some advice?
Thanks!

I wonder if there are only two species:human and mice can be choosed in add_ENSID function, what can I do when my species is zebrafish

Hi junyao,
Thanks for your excellent work. I can use bulk ATAC-seq data and scRNA-seq data to construck a developmental gene regulatory network.
Now I am preparing the files needed for IReNA, while my scRNA-seq data has nine time points and ~41000 cells and ~99000 genes. The matrix is too huge to run the monocle pseudo time analysis with error as follow. Then I wonder whether I could use a 3000 or 5000 subset cells for the pseudotime analysis by using this command.
sample_cell=sample(colnames(rds),3000,replace = FALSE)
Hope to your reply. Thanks for your time.

Hi, thanks for the great job! I get an error hoping for your help.
In terminal
sudo sh ./fimoall.sh

Or rstudio

### run the following codes in the R under linux environment
refdir='./Downloads/package/IReNA/mm39.fa.gz'
fimodir <- './meme' (I am not sure this is right?)
outputdir1 <- './irena/'
motifdir <- './Downloads/motif/'
find_motifs_targetgenes(gene_tss,motif1,refdir,fimodir,outputdir1,motifdir)
### run fimo_all script in shell
shell_code <- paste0('echo "password" | sudo -S sh ',outputdir1,'fimo/fimoall.sh')
system(shell_code,wait=TRUE) 

./irena/fimo/ENSMUSG00000024782/Fimo1.sh: 1: ./meme: Permission denied
..........
./irena/fimo/ENSMUSG00000024782/Fimo1.sh: 500: ./meme: Permission denied

I get a lot of .txt files with 0B size.
fimodir <- './meme' (I am not sure this is right?)

Hi, I now have the data (10x multiome) for the basic analysis done with Signac, and I want to use it to analyze the specific gene regulatory network. Is there any way to analyze it directly in Signac format? Or can I get the required input file by format conversion?
I will be appreciated it if you can reply me soon, Thank you all!

The file named "scATAC-seq.zip" cannot be found in the "IReNA-test-data" folder.

Hi,
I was following your tutorial and received the following warnings/error:

library(IReNA)
Loading required package: pheatmap
Loading required package: DDRTree
Loading required package: irlba
Loading required package: Matrix
Loading required package: RcisTarget
Registered S3 method overwritten by 'data.table':
  method           from
  print.data.table     
Warning: multiple methods tables found for ‘aperm’Warning: replacing previous import ‘BiocGenerics::aperm’ by ‘DelayedArray::aperm’ when loading ‘SummarizedExperiment’No methods found in package ‘BiocGenerics’ for requests: ‘as.vector’, ‘clusterEvalQ’, ‘parCapply’, ‘parRapply’, ‘unlist’ when loading ‘monocle’
Registered S3 methods overwritten by 'dbplyr':
  method         from
  print.tbl_lazy     
  print.tbl_sql     


expression_profile <- get_SmoothByBin_PseudotimeExp(seurat_with_time, Bin = 60, method = 'State')
Error in rowMeans(seurat_exp2_state[, PseudotimeBin1[i]:PseudotimeBin1[i + :
'x' must be an array of at least two dimensions
```
Would you give me some tips? Thanks.

Hi, do you have any suggestions for building TF motif datasets for other species, like Macaca fascicularis?
I see it in the tutorial user-defined motif dataset which should have the same format as these from TRANSFAC database., but I don't know how to prepare my own dataset.
Hope to your reply. Thanks for your time.

When I ran the tutorial of Regulatory network analysis through intergrating scRNA-seq data and scATAC-seq data, I can't found the file named P1_CM_3sample_seurat.rds.