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xu-lab / SINCERA

An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis
https://research.cchmc.org/pbge/sincera.html
GNU General Public License v3.0
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Interested in analyzing data generated by 10X CellRanger with SINCERA #11

Open veralow1990 opened 5 years ago

veralow1990 commented 5 years ago

Hi there! Could you please instruct me in importing data generated by 10X genomics CellRanger to SINCERA? I'm really eager to use the TF prediction function in SINCERA. Thank you so much!

yitongf commented 5 years ago

Hello, I'm having exactly the same problem!!! When I check their publication they said "The pipeline takes RNA-seq expression values (e.g., FPKM or TPM) from heterogeneous single cell populations as inputs". So I'm guessing it cannot read 10X data from cellranger directly... Please tell me if you have the solution, or if you have other opinions ;) Bw.

ShuyangZhao commented 5 years ago

The ChromiumTM Cell RangerTM pipeline produces processed gene-barcode matrices and primary results. By specifiying the pipeline output directory (or pipestance path), you can use the R kit to load these pipeline results into your local R environment. You can load the pipeline data by specifying a pipestance path in R as follows.

cellranger_pipestance_path <- "/path/to/your/pipeline/output/directory"
gbm <- load_cellranger_matrix(cellranger_pipestance_path)
analysis_results <- load_cellranger_analysis_results(cellranger_pipestance_path)