Package: cinaR 0.2.4

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_0.2.4.tar.gz
cinaR_0.2.4.zip(r-4.5)cinaR_0.2.4.zip(r-4.4)cinaR_0.2.4.zip(r-4.3)
cinaR_0.2.4.tgz(r-4.4-any)cinaR_0.2.4.tgz(r-4.3-any)
cinaR_0.2.4.tar.gz(r-4.5-noble)cinaR_0.2.4.tar.gz(r-4.4-noble)
cinaR_0.2.4.tgz(r-4.4-emscripten)cinaR_0.2.4.tgz(r-4.3-emscripten)
cinaR.pdf |cinaR.html✨
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

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

5.48 score 12 stars 50 scripts 205 downloads 14 exports 100 dependencies

Last updated 6 months agofrom:ff44a57de4. Checks:OK: 5 ERROR: 1 NOTE: 1. Indexed: yes.

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

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

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

Introduction to cinaR

E Onur Karakaslar

Rendered fromcinaR.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-05-22
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
run_enrichment	run_enrichment
scale_rows	scale_rows
show_comparisons	show_comparisons
verboseFn	verboseFn
Immune modules	vp2008