README.md

In warrenmcg/absSimSeq: RNA-Seq Simulation with Absolute Counts

absSimSeq

NOTE: A preprint is coming soon! If you choose to try this, any constructive feedback is greatly appreciated!

This package simulates RNA-Seq experiments with an explicit definition of the absolute RNA counts.

This package extends the polyester package by simulating an RNA-Seq using absolute RNA counts before converting the result into relative proportions (in TPMs and expected fragments) that are then used as input for polyester.

The basic workflow is the following: 1) Take an estimate of TPM values from a sleuth object. 2) Conceptually shift the unit from TPM to copy numbers per cell. 3) Simulate differential expression on the copy numbers 4) Convert the new copy numbers back to TPMs 5) Convert TPM values to expected reads per transcript 6) Simulate reads using the polyester (bioconductor page) package.

Usage

See the vignette for full details!

warrenmcg/absSimSeq documentation built on May 29, 2019, 9:57 a.m.