Man pages for mikelove/fishpond
Fishpond: downstream methods and tools for expression data
| addStatsFromCSV | Read statistics and nulls from CSV file |
| alevinEC | Construct a sparse matrix of transcript compatibility counts... |
| computeInfRV | Compute inferential relative variance (InfRV) |
| deswish | deswish: DESeq2-apeglm With Inferential Samples Helps |
| fishpond-package | Fishpond: downstream methods and tools for expression data |
| getTrace | Obtain a trace of inferential replicates for a sample |
| importAllelicCounts | Import allelic counts as a SummarizedExperiment |
| isoformProportions | Create isoform proportions from scaled data |
| labelKeep | Label rows to keep based on minimal count |
| loadFry | Load in data from alevin-fry USA mode |
| makeInfReps | Make pseudo-inferential replicates from mean and variance |
| makeSimSwishData | Make simulated data for swish for examples/testing |
| makeTx2Tss | Make a GRanges linking transcripts to TSS within gene |
| miniSwish | Helper function for distributing Swish on a subset of data |
| plotAllelicGene | Plot allelic counts in a gene context using Gviz |
| plotAllelicHeatmap | Plot allelic ratio heatmap |
| plotInfReps | Plot inferential replicates for a gene or transcript |
| plotMASwish | MA plot - log fold change over average counts |
| salmonEC | Construct a sparse matrix of transcript compatibility counts... |
| scaleInfReps | Scale inferential replicate counts |
| splitSwish | Function for splitting SummarizedExperiment into separate RDS... |
| swish | Swish method: differential expression accounting for... |
