2024 Elsevier Inc.To facilitate single-cell multi-omics analysis and improve reproducibility, we present single-cell pipeline for end-to-end data integration (SPEEDI), a fully automated end-to-end framework for
(G) Analysis of protein localization at the single cell level for four cell-cycle proteins regulated by localization or degradation. The red and blue bars indicate the fraction of single cells that were above our GFP fluorescence cutoff (mean intensity > log2(−11)) and assigned to Nucleus ...
nbt.3713-Challenges in long-term imaging and quantification of single-cell dynamics 热度: Design and Analysis of Single-Cell Sequencing Experiments 热度: Computational and experimental single cell biology techniques for the definition of cell type heterogeneity interplay and intracellular dynamics ...
A major informatic challenge in single cell RNA-sequencing analysis is the precise annotation of datasets where cells exhibit complex multilayered identities or transitory states. Here, we presentdevCellPya highly accurate and precise machine learning-enabled tool that enables automated prediction of cell...
dropkickcan be run as a command line tool or interactively with thescanpysingle-cell analysis suite. Usage from command line: dropkick run path/to/counts.h5ad Output will be saved in a new.h5adfile containing cell probability scores, labels, and model parameters. ...
centres and a more diverse patient population is required to disentangle socioeconomic, demographic and geographic effects on outcome models presented here. Whole-genome and RNA sequencing, as well as single-cell studies incorporating the tumour microenvironment43, are necessary to derive mechanistic ...
BH-SNE: Barnes-Hut-SNE; CC: Connected components; DIP: Dip-statistic test for multimodality; MDM: Microbial dark matter; OTU: Operational taxonomic unit; PCA: Principal component analysis; SCS: Single-cell sequencing; t-SNE: The-Distributed Stochastic Neighbor Embedding Acknowledgements Not applicable...
pipeline run parameters and then run the 11 phases of the pipeline in sequence. Some cells will display output figures generated by STREAMLINE. For example, scroll down to 'Phase 6: Statistics' and open the cell below the text 'Run Statistics Summary and Figure Generation'. Scrolling down ...
Next-generation sequencing data were analyzed using the VariantDx bioinformatics pipeline through alignment to the human reference genome assembly for the identification of sequence mutations, including single base substitutions (SBSs) and insertions/deletions (indels). Candidate variants were filtered through...
To test the procedures for automated single-particle analysis in RELION-4.0, we processed 12 data sets from the EMPIAR data base [38], using default parameters from relion_it.py, except for the experiment-specific parameters and the particle diameter as shown in Table 1. The 12 data sets we...