curatedAdipoChIP | Overview | Introduction | What is curatedAdipoChIP? | What is contained in curatedAdipoChIP? | What is curatedAdipoChIP for? | Installation | Docker image | Generating curatedAdipoChIP | Search starategy & data collection | Pre-processing | 1. Downloading data download_fastq | 2. Making a genome index make_index | 3. Dowinloading annotations get_annotation | 4. Aligning reads align_reads | 5. Calling peaks peak_calling | 6. Making a peakset get_peakset | 7. Counting reads in peaks count_features | 8. Quality assessment fastqc | Processing | Making a summarized experiment object peak_object | Exploring the peak_counts object | Summary of the studies in the dataset | Example of using curatedAdipoChIP | Motivation | Subsetting the object to samples and peaks of interest | Filtering low quality samples | Filtering peaks with low counts | Check sample reproducibility | Applying differential binding using DESeq2 | Next! | Citing the studies in this subset of the data | Citing curatedAdipoChIP | Session Info
Package: curatedAdipoChIP 1.29.0
Mahmoud Ahmed
curatedAdipoChIP: A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)
A curated dataset of publicly available ChIP-sequencing of transcription factors, chromatin remodelers and histone modifications in the 3T3-L1 pre-adipocyte cell line. The package document the data collection, pre-processing and processing of the data. In addition to the documentation, the package contains the scripts that was used to generated the data.
Authors:
curatedAdipoChIP_1.29.0.tar.gz
curatedAdipoChIP_1.29.0.tar.gz(r-4.7-any)curatedAdipoChIP_1.29.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
curatedAdipoChIP/json (API)
| # Install 'curatedAdipoChIP' in R: |
| install.packages('curatedAdipoChIP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mahshaaban/curatedadipochip/issues
On BioConductor:curatedAdipoChIP-1.29.0(data/experiment 3.24)curatedAdipoChIP-1.28.0(data/experiment 3.23)
experimentdataexperimenthubgeochipseqdatasequencingdatadatapkg
Last updated from:3bea9ced39. Checks:1 WARNING, 3 OK. Indexed: yes.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 218 | ||
| linux-devel | OK | 476 | ||
| source / vignettes | OK | 408 | ||
| linux-release | OK | 373 |
Exports:
Dependencies:abindAnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydplyrExperimentHubfastmapfilelockgenericsGenomicRangesgluehttrhttr2IRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsrlangRSQLiteS4ArraysS4VectorsSeqinfoSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 'curatedAdipoChIP' package | curatedAdipoChIP-package curatedAdipoChIP |
