https://github.com/bioconductor-source/wiggleplotr
Science Score: 26.0%
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Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- License: apache-2.0
- Language: HTML
- Default Branch: devel
- Size: 1.95 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
wiggleplotr
wiggleplotr is a tool to visualise RNA-seq read overage overlapping gene annotations. A key feature of wiggleplotr is that it is able rescale all introns of a gene to fixed length, making it easier to see differences in read coverage between neighbouring exons that can otherwise be too far away. Since wiggleplotr takes standard BigWig files as input, it can also be used to visualise read overage from other sequencing-based assays such as ATAC-seq and ChIP-seq.
Installation
This repostitory contains the development version of wiggleplotr. The latest stable version can be installed directly from Bioconductor: ```r
try http:// if https:// URLs are not supported
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("wiggleplotr") ```
Alternatively, you can still install the development version using devtools:
r
library("devtools")
devtools::install_github("kauralasoo/wiggleplotr")
However, the stable Bioconductor version is likely to be the best option for most people.
Getting started
See the vignette for instructions on how to get started.
Citation
If you use wiggleplotr for research, please cite the Bioconductor package directly: Alasoo K (2019). wiggleplotr: Make read coverage plots from BigWig files. R package version 1.8.0.
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
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Dependencies
- R >= 3.6 depends
- GenomeInfoDb * imports
- GenomicRanges * imports
- IRanges * imports
- S4Vectors * imports
- assertthat * imports
- cowplot * imports
- dplyr * imports
- ggplot2 >= 2.2.0 imports
- purrr * imports
- rtracklayer * imports
- AnnotationDbi * suggests
- AnnotationFilter * suggests
- EnsDb.Hsapiens.v86 * suggests
- GenomicFeatures * suggests
- TxDb.Hsapiens.UCSC.hg38.knownGene * suggests
- biomaRt * suggests
- ensembldb * suggests
- knitr * suggests
- org.Hs.eg.db * suggests
- rmarkdown * suggests
- testthat * suggests