fishpond
Differential expression and allelic analysis, nonparametric statistics
Science Score: 33.0%
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Keywords
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Repository
Differential expression and allelic analysis, nonparametric statistics
Basic Info
- Host: GitHub
- Owner: thelovelab
- Language: R
- Default Branch: devel
- Homepage: https://thelovelab.github.io/fishpond
- Size: 7.89 MB
Statistics
- Stars: 29
- Watchers: 2
- Forks: 10
- Open Issues: 1
- Releases: 1
Topics
Metadata Files
README.md
fishpond 
Fishpond: downstream methods and tools for expression data
Fishpond contains a method, swish(), for differential transcript and
gene expression analysis of RNA-seq data using inferential replicates.
Also the package contains utilities for working with Salmon,
alevin, and alevin-fry quantification data, including
loadFry().
Quick start
The following paradigm is used for running a Swish analysis:
y <- tximeta(coldata) # reads in counts and inf reps
y <- scaleInfReps(y) # scales counts
y <- labelKeep(y) # labels features to keep
set.seed(1) # for reproducibility
y <- swish(y, x="condition") # simplest Swish case
How does Swish work
Swish accounts for inferential uncertainty in expression estimates by averaging test statistics over a number of inferential replicate datasets, either posterior samples or bootstrap samples. This is inspired by a method called SAMseq, hence we named our method Swish, for "SAMseq With Inferential Samples Helps". Averaging over inferential replicates produces a different test statistic than what one would obtain using only point estimates for expression level.
For example, one of the tests possible with swish() is a correlation
test of expression level over a condition variable. We can visualize
the distribution of inferential replicates with plotInfReps():
The test statistic is formed by averaging over these sets of data:
p-values and q-values are computed through permutation of samples (see vignette for details on permutation schemes).
The Swish method is described in the following publication:
Zhu, A., Srivastava, A., Ibrahim, J.G., Patro, R., Love, M.I. "Nonparametric expression analysis using inferential replicate counts" Nucleic Acids Research (2019) 47(18):e105 PMC6765120
The SEESAW method for allelic expression analysis is described in the following preprint:
Euphy Wu, Noor P. Singh, Kwangbom Choi, Mohsen Zakeri, Matthew Vincent, Gary A. Churchill, Cheryl L. Ackert-Bicknell, Rob Patro, Michael I. Love. "Detecting isoform-level allelic imbalance accounting for inferential uncertainty" bioRxiv (2022) doi: 10.1101/2022.08.12.503785
Installation
This package can be installed via Bioconductor:
BiocManager::install("fishpond")
Funding
This work was funded by NIH NHGRI R01-HG009937.
Owner
- Name: The Love Lab
- Login: thelovelab
- Kind: organization
- Email: michaelisaiahlove [at] gmail
- Location: United States of America
- Website: https://mikelove.github.io
- Twitter: mikelove
- Repositories: 1
- Profile: https://github.com/thelovelab
Software produced by members of the Love Lab (UNC-Chapel Hill)
GitHub Events
Total
- Issues event: 1
- Watch event: 2
- Issue comment event: 3
- Push event: 6
- Pull request event: 2
Last Year
- Issues event: 1
- Watch event: 2
- Issue comment event: 3
- Push event: 6
- Pull request event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| mikelove | m****e@g****m | 384 |
| jgilis | j****s@u****e | 24 |
| Nitesh Turaga | n****a@g****m | 14 |
| DongzeHe | d****a@g****m | 11 |
| DongzeHE | 3****E | 9 |
| Steve Lianoglou | l****u@d****m | 6 |
| unknown | w****s@g****m | 4 |
| Anqi Zhu | a****u@l****u | 2 |
| J Wokaty | j****y@s****u | 2 |
| Mike Love | m****e | 2 |
| J Wokaty | j****y | 2 |
| k3yavi | a****a@c****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 18
- Total pull requests: 23
- Average time to close issues: 18 days
- Average time to close pull requests: about 23 hours
- Total issue authors: 14
- Total pull request authors: 7
- Average comments per issue: 3.22
- Average comments per pull request: 1.96
- Merged pull requests: 20
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 2
- Average time to close issues: 5 days
- Average time to close pull requests: 1 day
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 3.0
- Average comments per pull request: 1.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- mikelove (3)
- sunliang3361 (2)
- zhangjy859 (2)
- DrHogart (1)
- DongzeHE (1)
- qxxxd (1)
- smlchen (1)
- HenrikBengtsson (1)
- rsak-384 (1)
- ChristelKrueger (1)
- biozzq (1)
- AnnaAMonaco (1)
- JosephLalli (1)
- jeremymsimon (1)
Pull Request Authors
- DongzeHE (8)
- jgilis (8)
- Varix (2)
- an-altosian (2)
- k3yavi (1)
- lianos (1)
- JosephLalli (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 37,033 total
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: fishpond
Fishpond: downstream methods and tools for expression data
- Homepage: https://thelovelab.github.io/fishpond https://thelovelab.com/mikelove/fishpond
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/fishpond/inst/doc/fishpond.pdf
- License: GPL-2
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Latest release: 2.14.0
published 9 months ago
Rankings
Maintainers (1)
Dependencies
- GenomicRanges * imports
- IRanges * imports
- Matrix * imports
- S4Vectors * imports
- SingleCellExperiment * imports
- SummarizedExperiment * imports
- abind * imports
- graphics * imports
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- jsonlite * imports
- matrixStats * imports
- methods * imports
- qvalue * imports
- stats * imports
- svMisc * imports
- utils * imports
- AnnotationDbi * suggests
- DESeq2 * suggests
- EnsDb.Hsapiens.v86 * suggests
- GenomeInfoDb * suggests
- GenomicFeatures * suggests
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- data.table * suggests
- ensembldb * suggests
- knitr * suggests
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- org.Hs.eg.db * suggests
- pheatmap * suggests
- rmarkdown * suggests
- samr * suggests
- testthat * suggests
- tximeta * suggests
- tximportData * suggests
- actions/cache v2 composite
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