How to import read count matrix into CellDataSet object
Dear all,
I get stuck with something basic. I have a read count table (a matrix) and I want to import it into monocle. What is the format of feature data and pheno data that I need to use and what is the format of data matrix ?
Hello, I have a list of enhancers and the genes they target that looks like this for mm10 genome: Enhancer Target Gene 1: chr4_98727908_98728497 L1td1 …
Hi there, I know that we can use differentialGeneTest to find genes that are most differentially expressed across the states by using the formula "~State". …
Hi, I'm trying to follow tutorial 1 on http://cole-trapnell-lab.github.io/monocle-release/monocle3/#tutorial-1-learning-trajectories-with-monocle-3, but when I try to use the functions estimateSizeFactors() on my CellDataSet, I get the error …
I am studying the R package Monocle: There is function for analyzing Branches in Single-Cell Trajectories. I am confused that how to identify these trajeatories. …
I am trying to use single cell RNA seq (SE) data using moncole @ http://cole-trapnell-lab.github.io/monocle-release/docs/#installing-monocle I aligned data to GRCH38 run cufflink, However I could …
I am working with cuffdiff 2. Looking at the isoform.count_tracking file there are several columns of the form : > count, count_variance, count_uncertainty_var, count_dispersion_var, > …