Package: cinaR 0.2.6

Onur Karakaslar

cinaR: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles

Differential analyses and Enrichment pipeline for bulk 'ATAC-seq' data analyses. This package combines different packages to have an ultimate package for both data analyses and visualization of 'ATAC-seq' data. Methods are described in 'Karakaslar et al.' (2021) <doi:10.1101/2021.03.05.434143>.

Authors:Onur Karakaslar [aut, cre], Duygu Ucar [aut]

cinaR_0.2.6.tar.gz
cinaR_0.2.6.zip(r-4.7)cinaR_0.2.6.zip(r-4.6)cinaR_0.2.6.zip(r-4.5)
cinaR_0.2.6.tgz(r-4.6-any)cinaR_0.2.6.tgz(r-4.5-any)
cinaR_0.2.6.tar.gz(r-4.7-any)cinaR_0.2.6.tar.gz(r-4.6-any)
cinaR_0.2.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
cinaR/json (API)
NEWS

# Install 'cinaR' in R:

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

Bug tracker:https://github.com/eonurk/cinar/issues

Pkgdown/docs site:https://eonurk.github.io

Datasets:

bed - Example peaks from bone marrow of B6 mice
grch37 - Grch37
grch38 - Grch38
grcm38 - Grcm38
vp2008 - Immune modules

On CRAN:

atac-seq differential-analysis enrichment-analysis gene-sets

5.90 score 16 stars 50 scripts 296 downloads 16 exports 93 dependencies

Last updated from:882ce2920a. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	289
source / vignettes	OK	434
linux-release-x86_64	OK	343
macos-release-arm64	OK	231
macos-oldrel-arm64	OK	228
windows-devel	OK	215
windows-release	OK	214
windows-oldrel	OK	180
wasm-release	OK	287

Exports:cinaR color_values dot_plot filterConsensus GSEA heatmap_differential heatmap_var_peaks HPEA normalizeConsensus pca_plot prep_scATAC_cinaR prep_scATAC_seurat run_enrichment scale_rows show_comparisons verboseFn

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocManager BiocParallel Biostrings bit bit64 blob cachem cli codetools cowplot cpp11 crayon curl data.table DBI DelayedArray DESeq2 dplyr edgeR farver fastmap fastmatch fgsea formatR futile.logger futile.options genefilter generics GenomicRanges ggplot2 ggrepel glue gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl pheatmap pillar pkgconfig png preprocessCore R6 RColorBrewer Rcpp RcppArmadillo rlang RSQLite S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray statmod SummarizedExperiment survival sva sys tibble tidyselect utf8 vctrs viridisLite withr writexl XML xtable XVector

Introduction to cinaR

E Onur Karakaslar

Rendered fromcinaR.Rmdusingknitr::rmarkdownon May 10 2026.

Last update: 2026-02-02
Started: 2020-10-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
annotatePeaks	annotatePeaks
Example peaks from bone marrow of B6 mice	bed
cinaR	cinaR
color values	color_values
Differential Analyses	differentialAnalyses
dot_plot	dot_plot
filterConsensus	filterConsensus
Grch37	grch37
Grch38	grch38
Grcm38	grcm38
GSEA	GSEA
heatmap_differential	heatmap_differential
heatmap_var_peaks	heatmap_var_peaks
HPEA	HPEA
normalizeConsensus	normalizeConsensus
pca_plot	pca_plot
prep_scATAC_cinaR	prep_scATAC_cinaR
prep_scATAC_seurat	prep_scATAC_seurat
run_enrichment	run_enrichment
scale_rows	scale_rows
show_comparisons	show_comparisons
verboseFn	verboseFn
Immune modules	vp2008