This package provides statistical methods and other tools for working with Salmon and Alevin quantification of RNA-seq data. In particular, it contains the Swish non-parametric method for detecting differential transcript expression (DTE). Swish can also be used to detect differential gene expresion (DGE).
The main functions are:
scaleInfReps - scaling transcript or gene expression data
labelKeep - labelling which features have sufficient counts
swish - perform non-parametric differential analysis
isoformProportions - convert counts to isoform proportions
makeInfReps - create pseudo-inferential replicates
splitSwish - split Swish analysis across jobs with Snakemake
All software-related questions should be posted to the Bioconductor Support Site:
The code can be viewed at the GitHub repository, which also lists the contributor code of conduct:
Anqi Zhu, Avi Srivastava, Joseph G. Ibrahim, Rob Patro, Michael I. Love
Zhu, A., Srivastava, A., Ibrahim, J.G., Patro, R., Love, M.I. (2019) Nonparametric expression analysis using inferential replicate counts. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz622
Compression, makeInfReps and splitSwish:
Van Buren, S., Sarkar, H., Srivastava, A., Rashid, N.U., Patro, R., Love, M.I. (2020) Compression of quantification uncertainty for scRNA-seq counts. bioRxiv. https://doi.org/10.1101/2020.07.06.189639
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