Tag: CIBERSORTx

Phenotypic plasticity and genetic control in colorectal cancer evolution

Sample preparation and sequencing The method of sample collection and processing is described in a companion article (ref. 23). Sequencing and basic bioinformatic processing of DNA-, RNA- and ATAC-seq data are included there as well. Gene expression normalization and filtering The number of non-ribosomal protein-coding genes on the 23 canonical chromosome pairs…

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Choose more PC for the silhouette score, and run the deconvolution benchmark and see if it improves, out methods compared to cibersortX #14

Jianwu1 @stemangiola Finalised benchmark: using new tree (treg as a sibling to t_helper) and the tip nodes for non_hierarchical and cibersortx: PCA as reduction method; Overall hierarchical_pairwise_contrast_bayes_silhouette_penalty gives cell signatures that result in the lowest median deconvolution error, it’s ranked first in dim=4 and dim=10, ranked third in dim=2, and…

Continue Reading Choose more PC for the silhouette score, and run the deconvolution benchmark and see if it improves, out methods compared to cibersortX #14

CIBERSORTxFractions ERROR: Could not read /src/outdir//temp.Fractions.simfracs.tsv

Hello, can anyone offer any insight into the following problem? I am trying to run the following CIBERSORTx function locally: docker run -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/data -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/outdir cibersortx/fractions –username <my_user_name> –token <my_token> –single_cell TRUE –refsample reference.txt –mixture rsem_mixture_TPM.tsv –fraction 0 –rmbatchSmode TRUE I get the following output to the terminal: >Running…

Continue Reading CIBERSORTxFractions ERROR: Could not read /src/outdir//temp.Fractions.simfracs.tsv

Integrating Bulk RNA-seq data with Single cell RNA seq data

Integrating Bulk RNA-seq data with Single cell RNA seq data 0 Hello all, recently, I had been trying to integrate bulk RNAseq data into single-cell data where I treat each sample in my bulk RNAseq data as a single cell and integrate it into the single-cell data based on the…

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