basilisk: a Bioconductor package for managing Python
environments

Lun, Aaron T. L.

doi:10.21105/joss.04742

Cited by 16 publications

(15 citation statements)

References 1 publication

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“…Next, fragments below a certain quality threshold and a size larger than a maximum provided by the user are removed before collapsing any duplicates (if present). This python-based capability was integrated into the scPipe R package using basilisk (20). Feature matrix construction can be via a .bed file provided to the workflow (e.g.…”

Section: Methodsmentioning

confidence: 99%

scPipe: An extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor

Amarasinghe,

Yang,

Voogd

et al. 2023

Preprint

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scPipe is a flexible R/Bioconductor package originally developed to analyse platform-independent single-cell RNA-Seq data. To expand its preprocessing capability to accommodate new single-cell technologies, we further developed scPipe to handle single-cell ATAC-Seq and multi-modal (RNA-Seq and ATAC-Seq) data. After executing multiple data cleaning steps to remove duplicated reads, low abundance features and cells of poor quality, a SingleCellExperiment object is created that contains a sparse count matrix with features of interest in the rows and cells in the columns. Quality control information (e.g. counts per cell, features per cell, total number of fragments, fraction of fragments per peak) and any relevant feature annotations are stored as metadata. We demonstrate that scPipe can efficiently identify "true" cells and provides flexibility for the user to fine-tune the quality control thresholds using various feature and cell-based metrics collected during data preprocessing. Researchers can then take advantage of various downstream single-cell tools available in Bioconductor for further analysis of scATAC-Seq data such as dimensionality reduction, clustering, motif enrichment, differential accessibility and cis-regulatory network analysis. The scPipe package enables a complete beginning-to-end pipeline for single-cell ATAC-Seq and RNA-Seq data analysis in R.

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Section: Methodsmentioning

confidence: 99%

scPipe: An extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor

Amarasinghe,

Yang,

Voogd

et al. 2023

Preprint

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“…More specifically, we first used the buildSNNGraph function from scran to build a shared-nearest neighbors graph with k = 50 nearest neighbors. This function is a wrapper for the makeSNNGraph function from the bluster package (Lun, 2022), which identifies k nearest neighbors between nuclei based on Euclidean distances between their gene expression profiles. Edges are drawn between nuclei with at least one shared-nearest neighbor using a rank-based weighting method (Xu & Su, 2015).…”

Section: Clusteringmentioning

confidence: 99%

Activity‐regulated gene expression across cell types of the mouse hippocampus

et al. 2023

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Activity‐regulated gene (ARG) expression patterns in the hippocampus (HPC) regulate synaptic plasticity, learning, and memory, and are linked to both risk and treatment responses for many neuropsychiatric disorders. The HPC contains discrete classes of neurons with specialized functions, but cell type‐specific activity‐regulated transcriptional programs are not well characterized. Here, we used single‐nucleus RNA‐sequencing (snRNA‐seq) in a mouse model of acute electroconvulsive seizures (ECS) to identify cell type‐specific molecular signatures associated with induced activity in HPC neurons. We used unsupervised clustering and a priori marker genes to computationally annotate 15,990 high‐quality HPC neuronal nuclei from N = 4 mice across all major HPC subregions and neuron types. Activity‐induced transcriptomic responses were divergent across neuron populations, with dentate granule cells being particularly responsive to activity. Differential expression analysis identified both upregulated and downregulated cell type‐specific gene sets in neurons following ECS. Within these gene sets, we identified enrichment of pathways associated with varying biological processes such as synapse organization, cellular signaling, and transcriptional regulation. Finally, we used matrix factorization to reveal continuous gene expression patterns differentially associated with cell type, ECS, and biological processes. This work provides a rich resource for interrogating activity‐regulated transcriptional responses in HPC neurons at single‐nuclei resolution in the context of ECS, which can provide biological insight into the roles of defined neuronal subtypes in HPC function.

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“…Clusters were manually annotated using a whole zebrafish single-cell transcriptome atlas (Farnsworth et al, 2020) as well zebrafish database of gene expression (ZFIN expression atlas: Thisse et al, 2001). Notably, a cluster optimization algorithm (Lun, 2022) identified resolution 0.7 as optimal. However in that case, msx1b+ fin epidermal cells co-clustered with pLLP cells; these populations separated into distinct clusters at resolution 0.8, which we used for further analysis.…”

Section: Quality Control and Unsupervised Clusteringmentioning

confidence: 99%

RhoA GEF Mcf2lb regulates rosette integrity during collective cell migration

Olson

Maxfield

Calistri

et al. 2023

Preprint

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During development, multicellular rosettes serve as important cellular intermediates in the formation of diverse organ systems. Multicellular rosettes are transient epithelial structures that are defined by the apical constriction of cells towards the rosette center. Due to the important role these structures play during development, understanding the molecular mechanisms by which rosettes are formed and maintained is of high interest. Utilizing the zebrafish posterior lateral line primordium (pLLP) as a model system, we identify the RhoA GEF Mcf2lb as a regulator of rosette integrity. The pLLP is a group of ~150 cells that migrates along the zebrafish trunk and is organized into epithelial rosettes; these are deposited along the trunk and will differentiate into sensory organs called neuromasts (NMs). Using single-cell RNA sequencing and whole-mount in situ hybridization, we showed thatmcf2lbis expressed in the pLLP during migration. Given the known role of RhoA in rosette formation, we asked whether Mcf2lb plays a role in regulating apical constriction of cells within rosettes. Live imaging and subsequent 3D analysis ofmcf2lbmutant pLLP cells showed disrupted apical constriction and subsequent rosette organization. This in turn resulted in a unique posterior Lateral Line phenotype: an excess number of deposited NMs along the trunk of the zebrafish. Cell polarity markers ZO-1 and Par-3 were apically localized, indicating that pLLP cells are normally polarized. In contrast, signaling components that mediate apical constriction downstream of RhoA, Rock-2a and non-muscle Myosin II were diminished apically. Altogether our results suggest a model whereby Mcf2lb activates RhoA, which in turn activates downstream signaling machinery to induce and maintain apical constriction in cells incorporated into rosettes.

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basilisk: a Bioconductor package for managing Python environments

Cited by 16 publications

References 1 publication

scPipe: An extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor

scPipe: An extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor

Activity‐regulated gene expression across cell types of the mouse hippocampus

RhoA GEF Mcf2lb regulates rosette integrity during collective cell migration

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