Tag: monocle3

Pan-hematopoietic Tox4 deletion reduces number of multipotential progenitors and impairs T cell development To understand the role of TOX4 in development, we generated Tox4 conditional knockout mice by the CRISPR-Cas9 methodology, and two loxP sites in the same orientation were inserted upstream and downstream of exons 4–6, respectively (Supplementary Fig. 1a). Considering…

Understanding learn_graph and ncenter in Monocle3 0 Hi all I have some questions about how Monocle3’s learn_graph function and ncenter parameters work. Background: I’m using Monocle3 to calculate trajectories for a dataset that consists of two cohorts – control and treated. Cleaning, dimensionality reduction and clustering were all done in…

Patient demographics were comparable across study cohorts From 22 January 2018 to 30 October 2020, a total of 122 patients from 18 sites in five countries were enrolled and randomized 2:1 to receive either motixafortide + G-CSF (80 patients) or placebo + G-CSF (42 patients) for HSPC mobilization (Fig. 1 and Extended Data Fig. 1a). Demographics between the two treatment…

Gene duplicate 1 Hi there, I am pretty new to single cell RNA seq and I am trying to learn by doing analysis for a data that has been published already. I am using monocle3 and I realized that some Ensembl IDs that are the same and I was wondering…

Trajectory analysis using Monocle3 with Seurat sub-clustering 0 Hi all, I am analyzing single cell RNA-seq data using Seurat and trying to do trajectory analysis using Monocle3. My analysis pipeline is below. # QC, NormalizeData, FindVariableFeatures for each sample independetly SelectIntegrationFeatures > FindIntegrationAnchors > IntegrateData > > ScaleData > RunPCA…

single-cell pseudotime analysis with monocle3 0 I have a question regarding pseudotime analysis. It seems, this analysis is done over only a certain cell type. However, I am wondering if we can apply it on all the cells we got from UMAP out of single-cell analysis. Can we? Also, If…

exchange the monocle data with Seurat 0 Hi everyone! I am pretty new to single cell RNA seq analysis. I am using monocle 3 for my analysis. the data file that I have downloaded has already normalized data and it was coming with ensembl ID and I was able to…

I have R 4.2.1 and the latest R studio build 554 on a macOS Monterey. I am trying to install monocle3 using the following : BiocManager::install(‘monocle3’) I get a really long error message BiocManager::install(“monocle3”) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.15…

Hey guys, maybe this question is obvious, but I have been trying to find an answer to this for a while now and just wanted to ask. I am analysing single cell data with scanpy and need to do differentiation trajectory prediction. My project leader (not a bioinformatician) recommended monocle3…

Licence: other No description or website provided. Projects that are alternatives of or similar to monocle3 dropEst Pipeline for initial analysis of droplet-based single-cell RNA-seq data Stars: ✭ 71 (-58.24%) Mutual labels:  single-cell-rna-seq StackedDAE Stacked Denoising AutoEncoder based on TensorFlow Stars: ✭ 23 (-86.47%) Mutual labels:  single-cell-rna-seq kmer-homology-paper Manuscript for functional prediction…

I am trying to run the Monocle3 function find_gene_modules() on a cell_data_set (cds) but am getting a variety of errors in this. I have not had any other issues before this. I am working with an imported Seurat object. My first error came back stating that the number of rows…

after run estimate_size_factors, data with active.assay = ‘integrated’ works too, but no deg in the result. > [email protected] = ‘integrated’ > cds_raw <- as.cell_data_set(seurat_object) Warning: Monocle 3 trajectories require cluster partitions, which Seurat does not calculate. Please run ‘cluster_cells’ on your cell_data_set object > cds <- cluster_cells(cds_raw) > pr_graph_test_res <-…

STICR lentiviral library preparation and validation We synthesized a high-complexity lentivirus barcode library that encodes approximately 60–70 million distinct oligonucleotide RNA sequences (STICR barcodes). STICR barcodes comprised three distinct oligonucleotide fragments cloned sequentially into a multicloning site within the 3′ UTR of an enhanced green fluorescent protein (eGFP) transgene under…

Which trajectory method is better !? 2 Hello I was engaged with a basic problem. I have dataset consist ~2000 cells and composed 8-9 clusters using Seurat package, then I transfer Seurat object to the Monocle. I tried monocle2 and monocle3. The problem is, how to make the trajectory ?…