Package: DEWSeq 1.21.0

bioinformatics team Hentze

DEWSeq: Differential Expressed Windows Based on Negative Binomial Distribution

DEWSeq is a sliding window approach for the analysis of differentially enriched binding regions eCLIP or iCLIP next generation sequencing data.

Authors:Sudeep Sahadevan [aut], Thomas Schwarzl [aut], bioinformatics team Hentze [aut, cre]

DEWSeq_1.21.0.tar.gz
DEWSeq_1.21.0.zip(r-4.5)DEWSeq_1.21.0.zip(r-4.4)DEWSeq_1.21.0.zip(r-4.3)
DEWSeq_1.21.0.tgz(r-4.4-any)DEWSeq_1.21.0.tgz(r-4.3-any)
DEWSeq_1.21.0.tar.gz(r-4.5-noble)DEWSeq_1.21.0.tar.gz(r-4.4-noble)
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DEWSeq.pdf |DEWSeq.html✨
DEWSeq/json (API)
NEWS

# Install 'DEWSeq' in R:

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

Bug tracker:https://github.com/embl-hentze-group/dewseq/issues

Datasets:

SLBP_K562_w50s20 - ENCODE eCLIP data for SLBP in K562, low count filtered
slbpDds - ENCODE eCLIP data SLBP in K562
slbpRegions - ENCODE eCLIP data SLBP in K562
slbpVst - ENCODE eCLIP data SLBP in K562
slbpWindows - ENCODE eCLIP data SLBP in K562

On BioConductor:DEWSeq-1.21.0(bioc 3.21)DEWSeq-1.20.0(bioc 3.20)

sequencing generegulation functionalgenomics differentialexpression bioinformatics eclip ngs-analysis

5.48 score 5 stars 4 scripts 154 downloads 6 exports 71 dependencies

Last updated 2 months agofrom:93a7801c6c. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:DESeqDataSetFromSlidingWindows extractRegions filterCounts resultsDEWSeq toBED topWindowStats

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel cli codetools colorspace cpp11 crayon curl data.table DelayedArray DESeq2 fansi farver formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle locfit magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppArmadillo rlang S4Arrays S4Vectors scales snow SparseArray SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Analyzing eCLIP and iCLIP data with DEWSeq

Sudeep Sahadevan, Thomas Schwarzl

Rendered fromDEWSeq.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-10-17
Started: 2019-09-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
create DESeq data object	DESeqDataSetFromSlidingWindows
extract significant regions	extractRegions
filter count data	filterCounts
extract DEWseq results	resultsDEWSeq
ENCODE eCLIP data for SLBP in K562, low count filtered	SLBP_K562_w50s20
ENCODE eCLIP data SLBP in K562	slbpDds
ENCODE eCLIP data SLBP in K562	slbpRegions
ENCODE eCLIP data SLBP in K562	slbpVst
ENCODE eCLIP data SLBP in K562	slbpWindows
windows/regions to BED	toBED
stats for the top windows in each region	topWindowStats

Usage by other packages (reverse dependencies)