Tag: reactome.db

removeBatchEffect with non-linear model fit 0 @2289c15f Last seen 6 hours ago Germany Hello, I am attempting to use limma’s removeBatchEffect for visualization purposes (heatmat & PCA) while fitting non-linear models (splines) to my expression data in DESeq2. Given that my design is balanced, would this approach work within the…

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see ReactomePA. Reactome Pathway Analysis Bioconductor version: 2.12 This package provides functions for pathway analysis based on REACTOME pathway database. It will implement enrichment analysis, gene set enrichment analysis and functional modules detection. Author:…

DOI: 10.18129/B9.bioc.gatom   Finding an Active Metabolic Module in Atom Transition Network Bioconductor version: Release (3.18) This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module)…

Hi all, I’m trying to create a SPIA data file for all 483 xml files for the KEGG Orthology (KO) Database. I’m working with a non-model organism that is not supported by KEGG as it’s own organism, so I have to use the KEGG Orthology (KO) Database instead of a…

DOI: 10.18129/B9.bioc.famat   Functional analysis of metabolic and transcriptomic data Bioconductor version: Release (3.17) Famat is made to collect data about lists of genes and metabolites provided by user, and to visualize it through a Shiny app. Information collected is: – Pathways containing some of the user’s genes and metabolites…

DOI: 10.18129/B9.bioc.PCAN     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see PCAN. Phenotype Consensus ANalysis (PCAN) Bioconductor version: 3.15 Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes…

Tool:The script to install the required packages for gene expression analysis using DESeq2 for downstream analysis and visualization 0 if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) # Install Bioconductor packages BiocManager::install(‘DESeq2’) BiocManager::install(“apeglm”) BiocManager::install(“EnhancedVolcano”) BiocManager::install(“Glimma”) BiocManager::install(“ggrepel”) BiocManager::install(‘limma’) BiocManager::install(‘edgeR’) BiocManager::install(“reactome.db”) BiocManager::install(“AnnotationDbi”) # Install CRAN packages install.packages(‘tidyverse’) install.packages(‘ggplot2’) install.packages(“pheatmap”) R RNAseq installation DESeq2 •…

Tool:the script to install all the required packages for gene expression analysis using DESeq2 0 if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) # Install Bioconductor packages BiocManager::install(‘DESeq2’) BiocManager::install(“apeglm”) BiocManager::install(“EnhancedVolcano”) BiocManager::install(“Glimma”) BiocManager::install(“ggrepel”) BiocManager::install(‘limma’) BiocManager::install(‘edgeR’) BiocManager::install(“reactome.db”) BiocManager::install(“AnnotationDbi”) # Install CRAN packages install.packages(‘tidyverse’) install.packages(‘ggplot2’) install.packages(“pheatmap”) R RNAseq installation DESeq2 • 29 views Read more…

Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…

DOI: 10.18129/B9.bioc.methylGSA     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see methylGSA. Gene Set Analysis Using the Outcome of Differential Methylation Bioconductor version: 3.13 The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as…

Obtaining directionality of pathways 0 I am attempting to use R to extract biological pathway information from several different online databases (specifically KEGG, Wikipathways and Reactome) and use that information in a larger project I am working on where I am attempting to gauge levels of pathway functionality. An important…

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see neaGUI. An R package to perform the network enrichment analysis (NEA). Bioconductor version: 2.13 neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko…

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see reactome.db. A set of annotation maps for reactome Bioconductor version: 2.14 A set of annotation maps for reactome assembled using data from reactome Author: Willem Ligtenberg Maintainer: Willem Ligtenberg <willem.ligtenberg at openanalytics.eu> Citation…