Overview | Introduction | What is curatedAdipoRNA? | What is contained in curatedAdipoRNA? | What is curatedAdipoRNA for? | Installation | Docker image | Generating curatedAdipoRNA | Search strategy & 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. Counting features count_features | Quality assessment fastqc | Processing | Making Summarized experiment object make_object | Exploring the adipo_counts object | Summary of the studies in the dataset | Example of using curatedAdipoRNA | Motivation | Filtering low quality samples | Filtering low count genes | Applying differential expression using DESeq2 | Next! | Citing the studies in this subset of the data | Citing curatedAdipoRNA | Session Info
Package: curatedAdipoRNA 1.29.0
Mahmoud Ahmed
curatedAdipoRNA: A Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)
A curated dataset of RNA-Seq samples. The samples are MDI-induced pre-phagocytes (3T3-L1) at different time points/stage of differentiation. The package document the data collection, pre-processing and processing. In addition to the documentation, the package contains the scripts that was used to generated the data.
Authors:
curatedAdipoRNA_1.29.0.tar.gz
curatedAdipoRNA_1.29.0.tar.gz(r-4.7-any)curatedAdipoRNA_1.29.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
curatedAdipoRNA/json (API)
| # Install 'curatedAdipoRNA' in R: |
| install.packages('curatedAdipoRNA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mahshaaban/curatedadiporna/issues
Datasets:
- adipo_counts - Gene counts in differentiating adipocytes
On BioConductor:curatedAdipoRNA-1.29.0(data/experiment 3.24)curatedAdipoRNA-1.28.0(data/experiment 3.23)
experimentdatageornaseqdatasequencingdataadiposernaseqdatapkg
Last updated from:314a7a27a7. Checks:3 WARNING, 1 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 | 173 | ||
| linux-devel | WARNING | 284 | ||
| source / vignettes | OK | 308 | ||
| linux-release | WARNING | 265 |
Exports:
Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gene counts in differentiating adipocytes | adipo_counts |
| 'curatedAdipoRNA' package | curatedAdipoRNA-package curatedAdipoRNA |