Package: scPipeline 0.2.0.0

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'.

Authors:Viswanadham Sridhara [aut, cre]

scPipeline_0.2.0.0.tar.gz

scPipeline_0.2.0.0.tar.gz(r-4.5-noble)scPipeline_0.2.0.0.tar.gz(r-4.4-noble)
scPipeline_0.2.0.0.tgz(r-4.4-emscripten)
scPipeline.pdf |scPipeline.html✨
scPipeline/json (API)
NEWS

# Install 'scPipeline' in R:

install.packages('scPipeline', repos = c('https://sridhara-omics.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.70 score 7 exports 216 dependencies

Last updated 4 days agofrom:707dfc8239. Checks:3 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 08 2025
R-4.5-linux	OK	Mar 08 2025
R-4.4-linux	OK	Mar 08 2025

Exports:AnnotateCellsWithSingleR ConvertGeneIdentifiers ReactomeData SeuratLowDim SeuratMarkers SeuratPreprocess TransferAnnotations

Dependencies:abind alabaster.base alabaster.matrix alabaster.ranges alabaster.schemas alabaster.se AnnotationDbi AnnotationHub askpass assorthead base64enc batchelor beachmat BH Biobase BiocFileCache BiocGenerics BiocManager BiocNeighbors BiocParallel BiocSingular BiocVersion biomaRt Biostrings bit bit64 bitops blob bslib cachem caTools celldex cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir digest dotCall64 dplyr dqrng evaluate ExperimentHub fansi farver fastDummies fastmap filelock fitdistrplus FNN fontawesome formatR fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools gypsum h5mread HDF5Array here highr hms htmltools htmlwidgets httpuv httr httr2 ica igraph IRanges irlba isoband jquerylib jsonlite jsonvalidate KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval leidenbase lifecycle listenv lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI munsell nlme openssl parallelly patchwork pbapply pillar pkgconfig plogr plotly plyr png polyclip prettyunits progress progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML ReactomeGSA reshape2 ResidualMatrix reticulate rhdf5 rhdf5filters Rhdf5lib rlang rmarkdown ROCR rprojroot RSpectra RSQLite rsvd Rtsne S4Arrays S4Vectors sass ScaledMatrix scales scattermore sctransform scuttle Seurat SeuratObject shiny SingleCellExperiment SingleR sitmo snow sourcetools sp spam SparseArray sparseMatrixStats spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect tinytex UCSC.utils utf8 uwot V8 vctrs viridisLite withr xfun xml2 xtable XVector yaml zoo

Seurat_processing

Viswanadham Sridhara

Rendered fromSeurat_processing.Rmdusingknitr::rmarkdownon Mar 08 2025.

Last update: 2025-03-07
Started: 2025-03-07

Citation

Readme and manuals

Help Manual

Help page	Topics
Annotate cells in a Seurat object using SingleR with Celldex	AnnotateCellsWithSingleR
Convert Gene Identifiers in a Seurat Object	ConvertGeneIdentifiers
Reactome Data Analysis for Seurat Object	ReactomeData
Create a Low dimensional Seurat object from scaled seurat object	SeuratLowDim
A thresholded markers list for better calculation of DE genes	SeuratMarkers
Preprocess count data and create a Seurat object	SeuratPreprocess
Transfer annotations to Seurat clusters	TransferAnnotations