Science Score: 59.0%
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Found 7 DOI reference(s) in README -
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Repository
Exon-Intron Split Analysis (EISA) in R
Basic Info
- Host: GitHub
- Owner: fmicompbio
- Language: R
- Default Branch: devel
- Homepage: https://fmicompbio.github.io/eisaR/
- Size: 13.2 MB
Statistics
- Stars: 16
- Watchers: 5
- Forks: 4
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
eisaR: Exon-Intron Split Analysis (EISA) in R
Overview
Exon-intron split analysis (EISA) uses ordinary RNA-seq data to measure
changes in mature RNA and pre-mRNA reads across different experimental
conditions to quantify transcriptional and post-transcriptional regulation
of gene expression.
For details see Gaidatzis et al., Nat Biotechnol 2015. doi: 10.1038/nbt.3269.
eisaR implements the major steps of EISA in R.
In addition, it contains functionality for extracting spliced and unspliced
transcript sequences, as well as intron sequences (with similar options as
the BUSpaRse) package), from an
annotated genome. These sequences can be indexed and used, e.g., for
quantification in preparation for RNA velocity estimation.
Developed by:
- Michael Stadler
- Dimos Gaidatzis
- Lukas Burger
- Charlotte Soneson
Also a big "thank you" for contributions to:
Installation
To install eisaR from Bioconductor, you will need at least R 4.0 and Bioconductor 3.11, which is available on April 28, 2020. Then use the following within R (see also eisaR download page):
```
BiocManager is needed to install Bioconductor packages
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
Install eisaR
BiocManager::install("eisaR") ```
Functionality
All you need is RNA-seq data from at least two conditions (e.g. wildtype and
mutant). The eisaR package contains convenience functions to facilitate the
steps in an exon-intron split analysis, which consists of:
- preparing the annotation (exonic and gene body coordinate ranges)
- quantifying RNA-seq alignments in exons and introns
- calculating and comparing exonic and intronic changes across conditions
- visualizing the results
For the steps 1. and 2. above, this eisaR vignette makes use of Bioconductor
annotation and the QuasR package.
It is also possible to obtain count tables for exons and introns using some
other pipeline or approach, and directly start with step 3.
Reference
EISA has been described in:
"Analysis of intronic and exonic reads in RNA-seq data characterizes
transcriptional and post-transcriptional regulation."
Gaidatzis D., Burger L., Florescu M. and Stadler, M.B.
Nat Biotechnol. 2015; 33(7):722-9.
PubMed: 26098447, doi: 10.1038/nbt.3269
The functionality for extracting spliced and unspliced transcript sequences, as well as intron sequences, for use in RNA velocity analysis, has been described in:
"Preprocessing choices affect RNA velocity results for droplet scRNA-seq data." Soneson C., Srivastava A., Patro R. and Stadler, M.B. PLoS Comput Biol 2021; 17(1):e1008585. PubMed: 33428615, doi: 10.1371/journal.pcbi.1008585
Software status
| Platforms | OS | R CMD check | Coverage |
|:----------------:|:----------------:|:----------------:|:----------------:|
| GitHub Actions | Linux/Windows/macOS | 
| 
|
| Bioc (devel) | Multiple | 
| |
| Bioc (release) | Multiple | 
| |
Owner
- Login: fmicompbio
- Kind: user
- Repositories: 17
- Profile: https://github.com/fmicompbio
GitHub Events
Total
- Watch event: 1
- Delete event: 1
- Push event: 9
- Pull request event: 2
- Create event: 2
Last Year
- Watch event: 1
- Delete event: 1
- Push event: 9
- Pull request event: 2
- Create event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| mbstadler | s****l@g****m | 110 |
| Charlotte Soneson | c****n@g****m | 63 |
| Nitesh Turaga | n****a@g****m | 10 |
| J Wokaty | j****y | 2 |
| J Wokaty | j****y@s****u | 2 |
| Federico Marini | m****f@u****e | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 12
- Total pull requests: 28
- Average time to close issues: 20 days
- Average time to close pull requests: 10 days
- Total issue authors: 8
- Total pull request authors: 3
- Average comments per issue: 4.33
- Average comments per pull request: 0.96
- Merged pull requests: 27
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: about 6 hours
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- csoneson (4)
- bihuaf (2)
- HelloYiHan (1)
- jhyoon11 (1)
- DHGK (1)
- cadyyuheng (1)
- dongminshion (1)
- saketkc (1)
Pull Request Authors
- csoneson (25)
- federicomarini (2)
- mbstadler (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 13,207 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: eisaR
Exon-Intron Split Analysis (EISA) in R
- Homepage: https://github.com/fmicompbio/eisaR
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/eisaR/inst/doc/eisaR.pdf
- License: GPL-3
-
Latest release: 1.20.0
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.1 depends
- BiocGenerics * imports
- GenomicRanges * imports
- IRanges * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- edgeR * imports
- graphics * imports
- limma * imports
- methods * imports
- stats * imports
- utils * imports
- AnnotationDbi * suggests
- BSgenome * suggests
- BSgenome.Hsapiens.UCSC.hg38 * suggests
- BiocStyle * suggests
- Biostrings * suggests
- GenomicFeatures * suggests
- QuasR * suggests
- Rbowtie * suggests
- Rhisat2 * suggests
- ensembldb * suggests
- knitr * suggests
- rmarkdown * suggests
- rtracklayer * suggests
- testthat * suggests
- actions/cache v1 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- grimbough/bioc-actions/build-install-check v1 composite
- grimbough/bioc-actions/run-BiocCheck v1 composite
- grimbough/bioc-actions/setup-bioc v1 composite
- r-lib/actions/setup-pandoc v2 composite