It maintains a reproducible record (vignettes) of the data processing along with the package. Consumers of the data package can verify how the processing was done, increasing confidence in your data. It automates construction of the documentation and maintains a data set version and anmd5 fingerpr...
CITE-seq data generated for this manuscript is available to download and explore at https://atlas.fredhutch.org/nygc/multimodal-pbmc/. All CITE-seq and ECITE-seq raw data are available in GEO database under the accession number GEO: GSE164378. All raw sequencing data are deposited in the...
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This is implemented by using the function compute_lisi() from the R package lisi v1.0 [43, 44]. cLISI ranges from 1 to K, where K is the total number of cell types in the dataset. One indicates a neighborhood consisting exclusively of cells from a single cell type, while K ...
we apply an additional step for these two datasets to reduce the dimensionality of the datasets by screening out such features using Seurat package V5 package [9], which is to use local polynomial to fit the line between the log-variance and log-mean and then calculate the feature variance....
Integrating single-cell datasets produced by multiple omics technologies is essential for defining cellular heterogeneity. Mosaic integration, in which different datasets share only some of the measured modalities, poses major challenges, particularly regarding modality alignment and batch effect removal. Here...
To determine k and r, scBubbletree relies on the gap statistic method [17] as implemented in the R-package cluster (function clusGap, version 2.1.2). This functionality is implemented in scBubbletree’s functions get_k and get_r. The gap statistic compares the within cluster sum of squar...
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Each hutch is equipped with dedicated monitoring nodes that also subscribe to the multicasts to receive a fixed fraction of all events where each event includes all the detector and diagnostic data recorded from one X-ray pulse. The monitoring nodes copy the data to shared memory where the data...