Man pages for fishpond
Fishpond: differential transcript and gene expression with inferential replicates
| addStatsFromCSV | Read statistics and nulls from CSV file |
| computeInfRV | Compute inferential relative variance (InfRV) |
| deswish | deswish: DESeq2-apeglm With Inferential Samples Helps |
| fishpond-package | Downstream methods for Salmon and Alevin expression data |
| isoformProportions | Create isoform proportions from scaled data |
| labelKeep | Label rows to keep based on minimal count |
| makeInfReps | Make pseudo-inferential replicates from mean and variance |
| makeSimSwishData | Make simulated data for swish for examples/testing |
| miniSwish | Helper function for distributing Swish on a subset of data |
| plotInfReps | Plot inferential replicates for a gene or transcript |
| plotMASwish | MA plot |
| readEDS | readEDS - a utility function for quickly reading in Alevin's... |
| scaleInfReps | Scale inferential replicate counts |
| splitSwish | Function for splitting SummarizedExperiment into separate RDS... |
| swish | swish: SAMseq With Inferential Samples Helps |
