Single Cell RNA-Seq Simulations for Ntranos, Yi, et al., 2019

This figshare repo contains the kallisto quantification of single cell RNA-seq simulations, which were used to benchmark differential expression methods in Ntranos, Yi et al., Nature Methods, 2019 [https://www.nature.com/articles/s41592-018-0303-9, https://github.com/pachterlab/NYMP_2018/]. Use of these simulations is welcome, given proper citation to the manuscript.
There are three simulations from RSEM. Each simulation has two cell groups, 105 cells from a "null" group and 105 cells from a "perturbed" group. These cells are sorted accordingly in the .rds files (first 105 vs last 105).
1. In the correlated changes simulation (sims_genes), genes are chosen to be perturbed and all transcripts of that gene are perturbed.
2. In the independent changes simulation (sims_transcripts), transcripts and independently chosen to be perturbed.
3. In the experimental simulation (sims_exp), effect sizes are derived from an experiment using DESeq2, and then transcripts within a gene are chosen to be perturbed with the same effect-sizes (matched by rank-order) as detected in experiment.
Files:- perturb.tsv list the perturbed genes / transcripts and their effect sizes.- tximport.rds and tx_tximport.rds provide the transcript counts and gene counts, accordingly.-pseudo_batch contains the directory of TCCs. matrix.tsv is the matrix of TCCs pertaining to the 210 cells. matrix.ec is a EC to transcript/TCC mapping. For more information on TCCs, consult the manuscript or ask questions at https://github.com/pachterlab/NYMP_2018.
Finally, we include a splatter simulation of 2 cell groups.The splat directory contains:- splat.rds which is the splatter object, containing the parameterization of the splatter simulation. Reading this file requires the splatter R library and its dependencies. 300 total cells were simulated; 105 cells from each cell group was taken and used benchmarking in our manuscript.- the transcript counts table (counts.rds) and its corresponding gene counts table (genecounts.rds). - perturb.tsv lists the perturbed transcripts.