Package: DEWSeq 1.27.0
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:
DEWSeq_1.27.0.tar.gz
DEWSeq_1.27.0.zip(r-4.7)DEWSeq_1.27.0.zip(r-4.6)DEWSeq_1.27.0.zip(r-4.5)
DEWSeq_1.27.0.tgz(r-4.6-any)DEWSeq_1.27.0.tgz(r-4.5-any)
DEWSeq_1.27.0.tar.gz(r-4.7-any)DEWSeq_1.27.0.tar.gz(r-4.6-any)
DEWSeq_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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
- 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-1.27.0(bioc 3.24)DEWSeq-1.26.0(bioc 3.23)
sequencinggeneregulationfunctionalgenomicsdifferentialexpressionbioinformaticseclipngs-analysis
Last updated from:4b6691240d. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 190 | ||
| linux-devel-x86_64 | NOTE | 386 | ||
| source / vignettes | OK | 333 | ||
| linux-release-x86_64 | NOTE | 347 | ||
| macos-release-arm64 | NOTE | 181 | ||
| macos-oldrel-arm64 | NOTE | 188 | ||
| windows-devel | NOTE | 271 | ||
| windows-release | NOTE | 282 | ||
| windows-oldrel | NOTE | 261 | ||
| wasm-release | OK | 155 |
Exports:DESeqDataSetFromSlidingWindowsextractRegionsfilterCountsresultsDEWSeqtoBEDtopWindowStats
Dependencies:abindBHBiobaseBiocGenericsBiocParallelclicodetoolscpp11data.tableDelayedArrayDESeq2farverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglambda.rlatticelifecyclelocfitMatrixMatrixGenericsmatrixStatsR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppArmadillorlangS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySummarizedExperimentvctrsviridisLitewithrXVector
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 |
