Seurat to Trajectory Analysis
I want to do trajectory analysis using https://dynverse.org/users/2-quick_start/
I dont know how to extract the inputs required for dynverse from seurat object
scrna
seurat
pseudotime
trajectory
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
SlingShot and Subsetting data
written by carolofharvest •Hello , I want to use slingshot package for trajectory analysis but before doing that I need to subset my annotated data to remove some …
-
Monocle3 transition to seurat
written by odi •I know to transition from Seurat to monocle3 one has to use library(Seurat Wrappers) and then use the function: as.cell_data_set(seuratobject). But, after reclustering in monocle3, …
-
Right assay and slot for the extraction of normalized data after "sct normalization" and "anchor b…
written by Omics data miningHello everyone I am using Seurat for single cell data analysis. I used SCTransform for normalization follows by anchor based integration method for integration of …
-
loom file for rna velocity
written by Chironex •hi all, i'm trying to do a rna velocity analysis on a seurat object. I saw that loom files with spliced and unspliced transcripts are …
-
FASTA to Seurat Object
written by AbsaR •I want to create seurat object from fasta files. I have illumina sequences, 2 .fasta files for each samples..... any pipeline to follow ?
-
SRA dataset to Seurat Object
written by AbsaR •I have [this dataset][1] downloaded in fasta files using SRA toolkit in windows. How can I 1. merge all lane1 (fasta1) files into 1 file? …
-
Sub clustering from Seurat Object
written by AbsaR •I want to create a sub-cluster and then plot it from a Seurat Object. For example from a group of different cell types I want …
-
seurat, subcluster and trajectory analysis (Monocle 3)
written by joonhong kwon •Hi all, I am analyzing single cell RNA-seq data using Seurat and would like the follow up the analysis with cell trajectory analysis using Monocle3. …
-
Volcano 3D plot on single cell seurat data ?
written by Ondina •I'm currently searching for a way of using volcano3D on single cell data analyzed with Seurat. Volcano3D looks like a fun and interesting method for …
-
%% error in Rstudio
written by AbsaR •```r dc.markers %>% group_by(cluster) %>% top_n(2, wt = avg_logFC) ``` the above code is giving error even after using dplyr and matrix libraries in seurat …
https://satijalab.org/seurat/articles/essential_commands.html#data-access-1