Tag: MOFA

Japan to Require TB Test for Tourists from 6 Countries, Including Indonesians

TEMPO.CO, Jakarta – The Japanese government will require tourists from Indonesia and five other countries to take tuberculosis (TB) tests before entering Japan beginning in 2024. The tests are intended for tourists planning to visit for more than three months. This information was conveyed by Health Minister Keizo Takemi last…

Continue Reading Japan to Require TB Test for Tourists from 6 Countries, Including Indonesians

Metaproteogenomic analysis of saliva samples from Parkinson’s disease patients with cognitive impairment

Characteristics of participants and analyses A total of 115 individuals (43 PDD, 45 PD-MCI) and 27 HC were included in this study. Both 16 S rRNA gene amplicon sequencing based microbiome analysis and metaproteomics profiling were performed for all salivary samples collected from the participants (Fig. 1). Fig. 1: Experimental overview….

Continue Reading Metaproteogenomic analysis of saliva samples from Parkinson’s disease patients with cognitive impairment

Uncovering the relationship between gut microbial dysbiosis, metabolomics, and dietary intake in type 2 diabetes mellitus and in healthy volunteers: a multi-omics analysis

After processing the data, 20 control samples and 21 Type 2 Diabetes Mellitus samples contained data from all three collected assays (bacteriome, mycobiome, metabolome). The bacteriome data comprised on average 9534 contigs (s.d. ± 3465), ranging from 2032 to 18,320 contigs (786 ASVs). The mycobiome data contained on average 5450 contigs (s.d. ± 4964),…

Continue Reading Uncovering the relationship between gut microbial dysbiosis, metabolomics, and dietary intake in type 2 diabetes mellitus and in healthy volunteers: a multi-omics analysis

Help with Mofa2

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”)) {…

Continue Reading Help with Mofa2

Top 25 Bioconductor Interview Questions and Answers

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,…

Continue Reading Top 25 Bioconductor Interview Questions and Answers

`MOFAobject@expectations` is empty list

`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 =…

Continue Reading `MOFAobject@expectations` is empty list

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

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…

Continue Reading Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

single cell multi-modal data (CITEseq) batch correction

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…

Continue Reading single cell multi-modal data (CITEseq) batch correction

Spatial multiomics map of trophoblast development in early pregnancy

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…

Continue Reading Spatial multiomics map of trophoblast development in early pregnancy

Spatial components of molecular tissue biology

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…

Continue Reading Spatial components of molecular tissue biology

Bug#991859: BioConductor MOFA2 needs basilisk

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…

Continue Reading Bug#991859: BioConductor MOFA2 needs basilisk

Feature selection

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…

Continue Reading Feature selection