Are || and ! ## [70] labeling_0.4.2 rlang_1.0.6 reshape2_1.4.4 If I want to select a subset of data in R, I can use the subset function. d, Frequency of S+ Bm cells was measured by flow cytometry and separated by mild (acute, n=40; month 6, n=39; month 12, n=11) and severe COVID-19 (acute, n=19; month 6, n=22; month 12, n=6). Many thanks in advance. I'm writing here to be sure to receive an email when somebody will post an explanation here :-). 1 Answer Sorted by: 1 With a little bit of workaround: i) Add a new column to the data slot (only because your original subset () call does so but it can be raw counts or any other data matrix in your Seurat object). Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 1b and Extended Data Fig. Sorted B cells were analyzed by scRNA-seq using the commercial 5 Single Cell GEX and VDJ v1.1 platform (10x Genomics). ), A vector of cell names to use as a subset. b, N+ (left) and S+ (right) Bm cell frequencies were determined in paired blood and tonsils of SARS-CoV-2-vaccinated (n=8) and SARS-CoV-2-recovered individuals (n=8). after integration, I subsetted my cells of interest using the integrated assay, and I still see apparent batch effects. ## Conversely, S+ CD21+ Bm cell subsets became predominant at month 6 post-second dose (Extended Data Fig. Also, please provide a reproducible example data for testing, dput (myData). Following subtraction of raw counts of baiting-negative control from those of all other antigen-baiting constructs in every cell, cutoffs for background binding levels were manually determined for every construct by inspection of bimodal distributions of count frequencies across all cells, and all binding counts below thresholds were set to zero and classified as nonbinding. Notice also that I have to use | as I want to compare each element of bf11 against 1, 2, and 3, in turn. Improving performance in multiple Time-Range subsetting from xts? Asking for help, clarification, or responding to other answers. Bm cells are colored by cluster (f, left), tissue origin (f, right) or SWT binding (g). 565), Improving the copy in the close modal and post notices - 2023 edition, New blog post from our CEO Prashanth: Community is the future of AI. how to make a subset of cells expressing certain gene in seurat R New blog post from our CEO Prashanth: Community is the future of AI, Improving the copy in the close modal and post notices - 2023 edition, Manually define clusters in Seurat and determine marker genes, Trim Seurat object to contain expression info only for selected genes, Seurat VlnPlot presenting expression of multiple genes in a single cluster. The following tutorial is designed to give you an overview of the kinds of comparative analyses on complex cell types that are possible using the Seurat integration procedure. ## [1] systemfonts_1.0.4 sn_2.1.0 plyr_1.8.8 Cheers, all look forward to learning more on this when the devs respond. high.threshold = Inf, Hoehn, K. B., Pybus, O. G. & Kleinstein, S. H. Phylogenetic analysis of migration, differentiation, and class switching in B cells. original object. Looking for job perks? | SetIdent(object = object, cells.use = 1:10, ident.use = "new.idents") | Idents(object = object, cells = 1:10) <- "new.idents" | J. Clin. Hi All, As one can see in the pic below, the quality is quite different in each of the duplicated conditions. Med. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide.
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