Tag: MOFA

Hi Biostars friends, I try to run this tutorial on my multiome data. The error I got mean my for loop tried to reach an index seem doesn’t exist but don’t know how to troubleshoot. Would you please have a suggestion? Thank you so much! for (i in c(“distal”,”promoter”)) {…

Bioconductor is an open-source software project that provides tools for the analysis and comprehension of high-throughput genomic data. It’s a powerful tool, widely used in bioinformatics and computational biology to process and analyze intricate biological data. Bioconductor’s strength lies in its vast array of packages specifically tailored for genomics research,…

`MOFAobject@expectations` is empty list 0 Hello I run the tutorial (raw.githack.com/bioFAM/MOFA2_tutorials/master/R_tutorials/CLL.html) library(MOFA2) library(MOFAdata) library(data.table) library(ggplot2) library(tidyverse) utils::data(“CLL_data”) MOFAobject <- create_mofa(CLL_data) MOFAobject data_opts <- get_default_data_options(MOFAobject) model_opts <- get_default_model_options(MOFAobject) model_opts$num_factors <- 15 train_opts <- get_default_training_options(MOFAobject) train_opts$convergence_mode <- “slow” train_opts$seed <- 42 MOFAobject <- prepare_mofa(MOFAobject, data_options = data_opts, model_options = model_opts, training_options =…

Roy, S. et al. Celebrating 20 years of genetic discoveries in legume nodulation and symbiotic nitrogen fixation. Plant Cell 32, 15–41 (2020). Article  CAS  PubMed  Google Scholar  Roux, B. et al. An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser‐capture microdissection coupled to RNA…

single cell multi-modal data (CITEseq) batch correction 0 I’m working with a BD Rhabsody AbSeq data set containting a targeted scRNA and surfce protein (ADT) layer measured in two batches. In general I aim to integrate both modalities (e.g. MOFA+ or SeuratV4) for a joined analysis. While I perform QC…

Human samples Placental and decidual samples used for the in vivo and in vitro profiling were obtained from elective terminations from: The MRC and Wellcome-funded Human Developmental Biology Resource (HDBR, www.hdbr.org), with appropriate maternal written consent and approval from the Fulham Research Ethics Committee (REC reference 18/LO/0822) and Newcastle and…

1. Okabe, Y. & Medzhitov, R. Tissue biology perspective on macrophages. Nat. Immunol. 17, 9–17 (2016). CAS PubMed  Google Scholar  2. Xia, C., Fan, J., Emanuel, G., Hao, J. & Zhuang, X. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc. Natl Acad. Sci. USA…

Hi Dirk, On Sun, Sep 19, 2021 at 03:45:57PM -0500, Dirk Eddelbuettel wrote: > > | I’m thinking about a “fake-basilisk” like r-cran-bh or r-bioc-zlib. > > I had a similar thought. I am also friends with the author of it. > > They are doing ‘The Right Thing’ there…

Feature selection 0 Hello, I am starting out with bulk ATAC data as bed files that include the read counts. I want to use this data for a package called MOFA, which requires these preprocessing steps: Normalisation: For count-based data such as RNA-seq or ATAC-seq we recommend size factor normalisation…