Package: REDseq 1.53.0

Lihua Julie Zhu

REDseq: Analysis of high-throughput sequencing data processed by restriction enzyme digestion

The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.

Authors:Lihua Julie Zhu, Junhui Li and Thomas Fazzio

REDseq_1.53.0.tar.gz
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REDseq.pdf |REDseq.html✨
REDseq/json (API)

# Install 'REDseq' in R:

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

Datasets:

example.REDseq - An example sequencing dataset from a restoration enzyme digestion (RED) experiment
example.assignedREDseq - An example assigned REDseq dataset
example.map - An example REmap dataset

On BioConductor:REDseq-1.53.0(bioc 3.21)REDseq-1.52.0(bioc 3.20)

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

sequencing sequencematching preprocessing

3.48 score 15 scripts 338 downloads 1 mentions 8 exports 123 dependencies

Last updated 5 months agofrom:c53b524b48. Checks:1 OK, 7 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 28 2025
R-4.5-win	NOTE	Feb 28 2025
R-4.5-mac	NOTE	Feb 28 2025
R-4.5-linux	NOTE	Feb 28 2025
R-4.4-win	NOTE	Feb 28 2025
R-4.4-mac	NOTE	Feb 28 2025
R-4.3-win	NOTE	Feb 28 2025
R-4.3-mac	NOTE	Feb 28 2025

Exports:assignSeq2REsite binom.test.REDseq buildREmap compareREDseq distanceHistSeq2RE plotCutDistribution summarizeByRE summarizeBySeq

Dependencies:abind AnnotationDbi AnnotationFilter askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome BSgenome.Celegans.UCSC.ce2 cachem ChIPpeakAnno cli codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray digest dplyr ensembldb fansi farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue graph gtable hms httr httr2 InteractionSet IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime multtest munsell nlme openssl pillar pkgconfig plogr png prettyunits progress ProtGenerics purrr pwalign R6 rappdirs RBGL RColorBrewer Rcpp RcppThread RCurl regioneR restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales snow SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils universalmotif utf8 vctrs VennDiagram viridisLite withr XML xml2 XVector yaml

REDseq Vignette

Rendered fromREDseq.Rnwusingutils::Sweaveon Feb 28 2025.

Last update: 2021-03-10
Started: 2013-10-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
REDseq	REDseq-package REDseq
Assign mapped sequence tags to corresponding restriction enzyme (RE) cut sites	assignSeq2REsite
Binomial test for REDseq dataset	binom.test.REDseq
Build a genome wide cut site map for a Restriction Enzyme (RE)	buildREmap
Compare two RED Sequencing Dataset	compareREDseq
Plot the distance distribution from sequence to the associated RE sites	distanceHistSeq2RE
an example assigned REDseq dataset	example.assignedREDseq
an example REmap dataset	example.map
an example sequencing dataset from a restoration enzyme digestion (RED) experiment	example.REDseq
plot cut frequencies of RE sites along a given chromosome	plotCutDistribution
Output count/weight summary by restriction enzyme cut site ID (REid)	summarizeByRE
Output count/weight summary by sequences	summarizeBySeq