Showing 9 of total 9 results (show query)
bioc
singleCellTK:Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.
Maintained by Joshua David Campbell. Last updated 22 days ago.
singlecellgeneexpressiondifferentialexpressionalignmentclusteringimmunooncologybatcheffectnormalizationqualitycontroldataimportgui
181 stars 10.16 score 252 scriptsbioc
epiregulon:Gene regulatory network inference from single cell epigenomic data
Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.
Maintained by Xiaosai Yao. Last updated 2 months ago.
singlecellgeneregulationnetworkinferencenetworkgeneexpressiontranscriptiongenetargetcpp
12 stars 6.53 score 17 scriptsbioc
alabaster.se:Load and Save SummarizedExperiments from File
Save SummarizedExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
Maintained by Aaron Lun. Last updated 5 months ago.
6.39 score 8 scripts 6 dependentsbioc
alabaster.sce:Load and Save SingleCellExperiment from File
Save SingleCellExperiment into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
Maintained by Aaron Lun. Last updated 5 months ago.
5.51 score 4 scripts 3 dependentsbioc
alabaster.spatial:Save and Load Spatial 'Omics Data to/from File
Save SpatialExperiment objects and their images into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
Maintained by Aaron Lun. Last updated 4 months ago.
5.02 score 5 scripts 1 dependentsbioc
alabaster.mae:Load and Save MultiAssayExperiments
Save MultiAssayExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
Maintained by Aaron Lun. Last updated 5 months ago.
4.78 score 5 scripts 1 dependentsbioc
alabaster.vcf:Save and Load Variant Data to/from File
Save variant calling SummarizedExperiment to file and load them back as VCF objects. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
Maintained by Aaron Lun. Last updated 5 months ago.
4.65 score 6 scripts 1 dependentsbioc
alabaster:Umbrella for the Alabaster Framework
Umbrella for the alabaster suite, providing a single-line import for all alabaster.* packages. Installing this package ensures that all known alabaster.* packages are also installed, avoiding problems with missing packages when a staging method or loading function is dynamically requested. Obviously, this comes at the cost of needing to install more packages, so advanced users and application developers may prefer to install the required alabaster.* packages individually.
Maintained by Aaron Lun. Last updated 5 months ago.
4.00 score 3 scripts
sridhara-omics
scPipeline:A Wrapper for 'Seurat' and Related R Packages for End-to-End Single Cell Analysis
Reports markers list, differentially expressed genes, associated pathways, cell-type annotations, does batch correction and other related single cell analyses all wrapped within 'Seurat'.
Maintained by Viswanadham Sridhara. Last updated 7 days ago.
2.70 score