fgsea An R-package for fast preranked gene set enrichment analysis (GSEA). The package implements a special algorithm to calculate the empirical enrichment score null distributions simultaneously for all the gene set sizes, which allows up to several hundred times faster execution time compared to original Broad implementation.
lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of targeted and untargeted lipidomics data. lipidomics results can be imported into lipidr as a numerical matrix or a Skyline export, allowing integration into current analysis frameworks. Data mining of lipidomics datasets is enabled through integration with Metabolomics Workbench API. lipidr allows data ...
Within each dataset, for each gene in our gene sets, we calculated a celltype specificity score using the EWCE R package (Github version committed July 29, 2019; Skene and Grant, 2016). For each pair of datasets, X and Y, we subtracted the mean microglial specificity score of Y from X.
Jan 02, 2020 · GSEA was performed with R package fgsea, with 10 5 permutations, as described above. Rapid Immunoprecipitation of Endogenous Protein (RIME) MCF7-ELF5-Isoform2 cells treated with Dox or vehicle from 24 hours after plating for 48 hours, cross-linked using 1% methanol-free formaldehyde (Thermo Fisher).
To recreate our findings in the manuscript, using the provided peak table from the GitHub repository, use the following code snippet. Ensure the "iHMP_48_metaboanalyst_input.csv" file is located in your current working directory.
MSigDB Collections The 31117 gene sets in the Molecular Signatures Database (MSigDB) are divided into 9 major collections, and several sub-collections.
Workshop Participation. The workshop will start with an introduction to the problem and the dataset using presentation slides. Following this, we will have a lab session on how one may tackle the problem of handling multiple conditions in trajectory inference and in downstream analysis involving differential progression and differential expression.
fgsea analysis. From the fgsea vignette “fast preranked gene set enrichment analysis (GSEA)”: This analysis is performed by: ranking all genes in the data set based on their correlation to the chosen phenotype, identifying the rank positions of all members of the gene set, and