Package: tidyseurat 0.8.2

tidyseurat: Brings Seurat to the Tidyverse

It creates an invisible layer that allow to see the 'Seurat' object as tibble and interact seamlessly with the tidyverse.

Authors:Stefano Mangiola [aut, cre], Maria Doyle [ctb]

tidyseurat_0.8.2.tar.gz
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tidyseurat.pdf |tidyseurat.html✨
tidyseurat/json (API)

# Install 'tidyseurat' in R:

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

Bug tracker:https://github.com/stemangiola/tidyseurat/issues

Datasets:

cell_type_df - Cell types of 80 PBMC single cells
pbmc_small_nested_interactions - Intercellular ligand-receptor interactions for 38 ligands from a single cell RNA-seq cluster.

On CRAN:

dplyr ggplot2 normalization pca purrr sct seurat single-cell single-cell-rna-seq tibble tidyr tidyverse transcripts tsne umap

9 exports 152 stars 5.08 score 147 dependencies 1 dependents 292 scripts 580 downloads

Last updated 2 months agofrom:9f9d2187d3. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 22 2024
R-4.5-win	NOTE	Aug 22 2024
R-4.5-linux	NOTE	Aug 22 2024
R-4.4-win	NOTE	Aug 22 2024
R-4.4-mac	NOTE	Aug 22 2024
R-4.3-win	NOTE	Aug 22 2024
R-4.3-mac	NOTE	Aug 22 2024

Exports:%>%aggregate_cells get_abundance_sc_long get_abundance_sc_wide join_features join_transcripts plot_ly tidy unnest_seurat

Dependencies:abind askpass base64enc BH bitops bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table deldir digest dotCall64 dplyr dqrng evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval leiden lifecycle listenv lmtest magrittr MASS Matrix matrixStats memoise mgcv mime miniUI munsell nlme openssl parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne sass scales scattermore sctransform Seurat SeuratObject shiny sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr survival sys tensor tibble tidyr tidyselect tinytex ttservice utf8 uwot vctrs viridisLite withr xfun xtable yaml zoo

Code for producing the figures in the article

Stefano Mangiola

Rendered fromfigures_article.Rmdusingknitr::knitron Aug 22 2024.

Last update: 2023-11-23
Started: 2020-11-04

Overview of the tidyseurat package

Stefano Mangiola

Rendered fromintroduction.Rmdusingknitr::knitron Aug 22 2024.

Last update: 2021-02-24
Started: 2020-08-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Aggregate cells	aggregate_cells aggregate_cells,Seurat-method
Order rows using column values	arrange arrange.Seurat
Coerce lists, matrices, and more to data frames	as_tibble as_tibble.Seurat
Efficiently bind multiple data frames by row and column	bind_cols bind_cols.Seurat bind_rows bind_rows.Seurat
Cell types of 80 PBMC single cells	cell_type_df
Count the observations in each group	add_count add_count.Seurat count count.Seurat
Keep distinct/unique rows	distinct distinct.Seurat
Extract a character column into multiple columns using regular expression groups	extract extract.Seurat
Keep rows that match a condition	filter filter.Seurat
Printing tibbles	formatting print print.Seurat
Mutating joins	full_join full_join.Seurat
Create a new 'ggplot' from a 'tidyseurat'	ggplot ggplot.Seurat
Get a glimpse of your data	glimpse glimpse.tidyseurat
Group by one or more variables	group_by group_by.Seurat
Split data frame by groups	group_split group_split.Seurat
Mutating joins	inner_join inner_join.Seurat
join_features	join_features join_features,Seurat-method
(DEPRECATED) Extract and join information for transcripts.	join_transcripts
Mutating joins	left_join left_join.Seurat
Create, modify, and delete columns	mutate mutate.Seurat
Nest rows into a list-column of data frames	nest nest.Seurat
Intercellular ligand-receptor interactions for 38 ligands from a single cell RNA-seq cluster.	pbmc_small_nested_interactions
Pivot data from wide to long	pivot_longer pivot_longer.Seurat
Initiate a plotly visualization	plotly plot_ly plot_ly.Seurat plot_ly.tbl_df
Extract a single column	pull pull.Seurat
Rename columns	rename rename.Seurat
returns variables from an expression	return_arguments_of
Mutating joins	right_join right_join.Seurat
Group input by rows	rowwise rowwise.Seurat
Sample n rows from a table	sample_frac sample_frac.Seurat sample_n sample_n.Seurat
Keep or drop columns using their names and types	select select.Seurat
Separate a character column into multiple columns with a regular expression or numeric locations	separate separate.Seurat
Subset rows using their positions	slice slice.Seurat slice_head slice_head.Seurat slice_max slice_max.Seurat slice_min slice_min.Seurat slice_sample slice_sample.Seurat slice_tail slice_tail.Seurat
Summarise each group down to one row	summarise summarise.Seurat summarize summarize.Seurat
Format the header of a tibble	tbl_format_header tbl_format_header.tidySeurat
tidy for `Seurat`	tidy tidy.Seurat
Unite multiple columns into one by pasting strings together	unite unite.Seurat
Unnest a list-column of data frames into rows and columns	unnest unnest.tidyseurat_nested unnest_seurat