Package: AnanseSeurat 1.2.0

Jos Smits

AnanseSeurat: Construct ANANSE GRN-Analysis Seurat

Enables gene regulatory network (GRN) analysis on single cell clusters, using the GRN analysis software 'ANANSE', Xu et al.(2021) <doi:10.1093/nar/gkab598>. Export data from 'Seurat' objects, for GRN analysis by 'ANANSE' implemented in 'snakemake'. Finally, incorporate results for visualization and interpretation.

Authors:Jos Smits [aut, cre, cph], Huiqing Jo Zhou [aut, fnd, cph]

AnanseSeurat_1.2.0.tar.gz
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AnanseSeurat.pdf |AnanseSeurat.html✨
AnanseSeurat/json (API)
NEWS

# Install 'AnanseSeurat' in R:

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

Bug tracker:https://github.com/jgasmits/ananseseurat/issues

On CRAN:

grn-analysis seurat-objects single-cell single-cell-atac-seq single-cell-rna-seq

4.90 score 8 stars 4 scripts 703 downloads 11 exports 171 dependencies

Last updated 1 years agofrom:3e46630a24. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 05 2024
R-4.5-win	OK	Nov 05 2024
R-4.5-linux	OK	Nov 05 2024
R-4.4-win	OK	Nov 05 2024
R-4.4-mac	OK	Nov 05 2024
R-4.3-win	OK	Nov 05 2024
R-4.3-mac	OK	Nov 05 2024

Exports:%>%config_scANANSE DEGS_scANANSE export_ATAC_maelstrom export_ATAC_scANANSE export_CPM_scANANSE Factor_Motif_Plot import_seurat_maelstrom import_seurat_scANANSE Maelstrom_Motif2TF per_cluster_df

Dependencies:abind askpass backports base64enc BH bitops boot broom bslib cachem car carData caTools cli cluster codetools colorspace commonmark corrplot cowplot cpp11 crayon crosstalk curl data.table deldir Deriv digest doBy dotCall64 dplyr dqrng evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome Formula fs future future.apply generics ggplot2 ggpubr ggrepel ggridges ggsci ggsignif 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 lme4 lmtest magrittr MASS Matrix MatrixModels matrixStats memoise mgcv microbenchmark mime miniUI minqa modelr munsell nlme nloptr nnet numDeriv openssl parallelly patchwork pbapply pbkrtest pillar pkgconfig plotly plyr png polyclip polynom progressr promises purrr quantreg R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra rstatix Rtsne sass scales scattermore sctransform Seurat SeuratObject shiny sitmo sourcetools sp spam SparseM spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable yaml zoo

introduction

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2023-01-25
Started: 2023-01-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
config_scANANSE	config_scANANSE
DEGS_scANANSE	DEGS_scANANSE
export_seurat_Maelstrom	export_ATAC_maelstrom
export_ATAC_scANANSE	export_ATAC_scANANSE
export_CPM_scANANSE	export_CPM_scANANSE
Factor_Motif_Plot	Factor_Motif_Plot
import_seurat_Maelstrom	import_seurat_maelstrom
import_seurat_scANANSE	import_seurat_scANANSE
Maelstrom_Motif2TF	Maelstrom_Motif2TF
per_cluster_df	per_cluster_df