Comments (2)
Hi @empiricalbayes, sure thing. Please note that this is an R script, not a TXT file, so it should be renamed (made TXT to comply with attachment requirements). This script is meant to be run from the command line with a single positional argument that is an integer between 1 and 5. This argument specifies the scaling factor to simulate (one of [0, 5, 10, 15, 20]). Note that this script takes quite a long time to run with CIBERSORT and bseq-sc comparisons. If commented out, Bisque and MuSiC should complete fairly quickly.
Arguments that should be noted/edited:
cibersort.path
is the path to the CIBERSORT.R file (retrieved by following https://shenorrlab.github.io/bseqsc/vignettes/pages/installation.html)seurat.rds
is an RDS file containing the single-cell/single-nuc object processed by Seuratseurat.marker.rds
is an RDS file containing the output ofSeurat::FindAllMarkers()
out.prefix
is the prefix for all cell composition output CSV files (it will output the ground truth as{prefix}.loo.true.csv
and a file for each method, scaling factor, and replication).
Here is the script: simulation_analysis.txt
Let me know if you run into any issues!
Thanks,
Brandon
from bisque.
Many thanks @brandonjew
from bisque.
Related Issues (20)
- Adipose dataset HOT 1
- how to prepare single cell input from multiple subjects as an input? HOT 1
- sim.data average proportions taking into account variation between replicates HOT 1
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- How to interpreter Bisque result HOT 7
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- visualization HOT 1
- Zero expression in selected genes HOT 4
- Input format HOT 1
- Error in out[[t]]$coefs : $ operator is invalid for atomic vectors HOT 1
- Lack of "ground truth"markers and estimation HOT 1
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- MarkerBasedDecomposition overlapping genes error HOT 3
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from bisque.