b2mehani
b2mehani
Hi @tiagochst and All, I am new with TCGA data and interested to plot 3D-Tsne using methylation data from TCGA. Below is my snippet for 2D Tsne plot. Can you...
Hi @BALuca and Team, I used CODEFACS for deconvolution and trying to use its output as an input for Ecotyper using tutorial_6. As recommended I used all the genes and...
Hi Team, I used CODEFACS for deconvolution and trying to use its output as an input for Ecotyper using tutorial_6. As recommended I used all the genes and their deconvolved...
Hi I am trying to run conicsmat and everytime I get an error at filterMatrix() My code is `gene_pos=getGenePositions(rownames(log2mat)) log2mat1=filterMatrix(log2mat,gene_pos[,"hgnc_symbol"],minCells=5)` ``` Error in UseMethod("filter_") : no applicable method for 'filter_'...
Hi @soerenmueller , @diazlab Can I regenerate the same plot using plotHistogram() in the given command: `hi=plotHistogram(l[,candRegions],log2mat,clusters=2,zscoreThreshold=2,patients) ` As every time I get a different set of clusters, can I...
Hi @soerenmueller and All, Is it possible with ConicSmat, we can select cells based on the presence or absence of a specific CNV?
Hi @diazlab and @soerenmueller I want to do the batch-correction for my samples before predicting CNVs using CONICSmat. Do you recommend any method for batch-correction as my histogram for the...
Hi @diazlab and @soerenmueller I want to predict tumor cells in Suva’s 2014 IDH wt Glioma dataset, for which I only have log2tpm values. How can we convert log2tpm to...
Hey @labrazil and @tiagochst I have scRNA Seq (10X genomics) data from a cancer and want to quantify the stemless indices for each cell type or cluster. Do you recommend...
I want to increase the size of the circles in the legend of SpatialDimPlot. How can I do that? I tried this "guides(colour = guide_legend(override.aes = list(size=10)))", but it didn’t...