Package: cicero 1.25.0

Hannah Pliner

cicero: Predict cis-co-accessibility from single-cell chromatin accessibility data

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends monocle 2 for use in chromatin accessibility data.

Authors:Hannah Pliner [aut, cre], Cole Trapnell [aut]

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cicero.pdf |cicero.html✨
cicero/json (API)
NEWS

# Install 'cicero' in R:

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

Datasets:

cell_data - Metadata for example cells in cicero_data
cicero_data - Example single-cell chromatin accessibility data
gene_annotation_sample - Example gene annotation information
human.hg19.genome - Chromosome lengths from human genome hg19

On BioConductor:cicero-1.25.0(bioc 3.21)cicero-1.24.0(bioc 3.20)

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

sequencing clustering cellbasedassays immunooncology generegulation genetarget epigenetics atacseq singlecell

5.80 score 314 scripts 541 downloads 2 mentions 19 exports 173 dependencies

Last updated 2 months agofrom:ff77b2cbc8. Checks:OK: 1 ERROR: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 24 2024
R-4.5-win	ERROR	Oct 31 2024
R-4.5-linux	ERROR	Nov 26 2024
R-4.4-win	ERROR	Oct 31 2024
R-4.4-mac	ERROR	Oct 31 2024
R-4.3-win	ERROR	Oct 31 2024
R-4.3-mac	ERROR	Oct 31 2024

Exports:aggregate_by_cell_bin aggregate_nearby_peaks annotate_cds_by_site assemble_connections build_gene_activity_matrix compare_connections df_for_coords estimate_distance_parameter find_overlapping_ccans find_overlapping_coordinates generate_ccans generate_cicero_models make_atac_cds make_cicero_cds normalize_gene_activities plot_accessibility_in_pseudotime plot_connections ranges_for_coords run_cicero

Dependencies:abind AnnotationDbi AnnotationFilter askpass assertthat backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biocViews biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster codetools colorspace combinat cpp11 crayon curl data.table DBI dbplyr DDRTree DelayedArray deldir dichromat digest dplyr ensembldb evaluate fansi farver fastICA fastmap filelock FNN fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glasso glue graph gridExtra gtable Gviz highr Hmisc hms HSMMSingleCell htmlTable htmltools htmlwidgets httr httr2 igraph interp IRanges irlba isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval leidenbase lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime monocle munsell nlme nnet openssl pheatmap pillar pkgconfig plogr plyr png prettyunits progress ProtGenerics proxy purrr R6 RANN rappdirs RBGL RColorBrewer Rcpp RcppEigen RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer Rtsne RUnit S4Arrays S4Vectors sass scales slam snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs VGAM viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

Single Cell ATAC-seq Analysis with Cicero

Hannah Pliner

Rendered fromwebsite.Rmdusingknitr::rmarkdownon Nov 24 2024.

Last update: 2023-02-23
Started: 2018-05-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
cicero	cicero-package cicero
Aggregate count CDS by groups of cells	aggregate_by_cell_bin
Make an aggregate count cds by collapsing nearby peaks	aggregate_nearby_peaks
Add feature data columns to fData	annotate_cds_by_site
Combine and reconcile cicero models	assemble_connections
Calculate initial Cicero gene activity matrix	build_gene_activity_matrix
Metadata for example cells in cicero_data	cell_data
Example single-cell chromatin accessibility data	cicero_data
Compare Cicero connections to other datasets	compare_connections
Construct a data frame of coordinate info from coordinate strings	df_for_coords
Calculate distance penalty parameter	estimate_distance_parameter
Find CCANs that overlap each other in genomic coordinates	find_overlapping_ccans
Find peaks that overlap a specific genomic location	find_overlapping_coordinates
Example gene annotation information	gene_annotation_sample
Generate cis-co-accessibility networks (CCANs)	generate_ccans
Generate cicero models	generate_cicero_models
Chromosome lengths from human genome hg19	human.hg19.genome
Make ATAC CDS object	make_atac_cds
Create cicero input CDS	make_cicero_cds
Make a symmetric square sparse matrix from data frame	make_sparse_matrix
Normalize gene activities	normalize_gene_activities
Plot accessibility by pseudotime	plot_accessibility_in_pseudotime
Plot connections	plot_connections
Construct GRanges objects from coordinate strings	ranges_for_coords
Run Cicero	run_cicero