destiny
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theislab
R package for single cell and other data analysis using diffusion maps
Hello, I have a code used by a previous user where there was an option whether to branch or not:  However, when I want to re-use this code I'm...
Hi, Thank you for providing this package, really love it. May I ask something? I found a very interesting thing, I run destiny many times using different data, why there...
hello - my lab has an R package that depends on destiny, pulling form bioconductor. our build off bioconductor devel is failing b/c it cannot download destiny. I'm not that...
Hi @flying-sheep I am currently attempting to install `destiny` from Bioconductor in R 4.0.3 (Bioc 3.12). The destiny package is only available in source form (I see destiny is failing...
Dear all, I would like to calculate a diffusion map with Gaussian kernels of various sigma with the full probability matrix (every cell to every cell). So, NO k nearest...
Hello, I'm curious if the DiffusionMap() function can be applied to bulk RNA sequencing data counts. Does doing so violate assumptions of normalization/noise control implemented in destiny, or do these...
Hi, I tried to install `destiny` by BiocManager but failed mainly because I couldn't install its dependencies. Here is my installation command lines : ```R BiocManager::install("destiny") ``` The following is...
Dear Devs, I have applied destiny::DiffusionMap to one of our internal datasets, providing the Seurat "data" slot normalized in a standard way as input (log2 (normalized counts + pseudocount)). When...
Hi, I have pre-processed my single cell RNA-seq dataset in seurat with its standard pipeline, including normalization, identification of highly variable features and scaling the data, and then I imported...
Hi, I would like to know if the parameter density_norm represents a choice to wether normalize or not the Gaussian kernel. I'm particularly interested if this is the case because...
