splatPop
Christina B. Azodi
Last updated: 2021-11-18
Checks: 6 1
Knit directory: KEJP_2020_splatPop/
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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (public/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 116e4a3 | cazodi | 2021-10-08 | update mean-variance plots for manuscript |
| Rmd | f2bf14a | cazodi | 2021-09-21 | update eqtl and de results |
| html | f2bf14a | cazodi | 2021-09-21 | update eqtl and de results |
| Rmd | f729828 | cazodi | 2021-08-31 | added time analysis up to 20k genes |
| html | f729828 | cazodi | 2021-08-31 | added time analysis up to 20k genes |
| html | 025596b | cazodi | 2021-08-31 | added coregulation example |
| Rmd | 9effdc2 | cazodi | 2021-08-31 | added coregulation example |
| Rmd | 7581c38 | cazodi | 2021-08-31 | added multichemistry batch effect example |
| html | 7581c38 | cazodi | 2021-08-31 | added multichemistry batch effect example |
| Rmd | 3f88d86 | cazodi | 2021-06-02 | conditional simulations added |
| html | 3f88d86 | cazodi | 2021-06-02 | conditional simulations added |
| Rmd | bd0c8b0 | cazodi | 2021-05-17 | updates to 10x neuroseq and ss2 ipsc examples |
| html | bd0c8b0 | cazodi | 2021-05-17 | updates to 10x neuroseq and ss2 ipsc examples |
| html | 0286c19 | cazodi | 2021-02-17 | re-knit after gitlab ci |
| Rmd | d24c101 | cazodi | 2021-02-17 | ipsc ss2 preprocessing |
| html | d24c101 | cazodi | 2021-02-17 | ipsc ss2 preprocessing |
| Rmd | b200a1f | cazodi | 2020-03-18 | removing accidental commits by christina… |
| Rmd | 9057b09 | cazodi | 2020-03-18 | Revert “initial repo change” |
| Rmd | 0c6d3c6 | cazodi | 2020-03-18 | initial repo change |
| Rmd | c57ac08 | Christina Azodi | 2019-11-26 | First init |
| Rmd | b1f309c | Davis McCarthy | 2019-02-06 | Updating template with improvements. |
| Rmd | d73fd37 | Davis McCarthy | 2019-01-10 | Initial commit |
Overview
This project demonstrates use cases for splatPop, an extension of the splat model implemented in Splatter, that allows for the simulation of population-scale single-cell RNA-sequencing data.
The splatPop functions are available in the splatter package (v1.18.1+), available in Bioconductor.
Key features:
- The simulation of known eQTL effects that give the simulated data realistic population structure.
- The ability to make these eQTL effects global, cell-group specific, or cohort specific.
- The simulation of differential gene expression effects between cell-groups or between cohorts within the population.
Data pre-processing
The empirical data used as reference data in this study were downloaded already processed by the original authors.
Analyses
The results presented in the paper were produced with the following reproducible analyses. They were generated by rendering the R Markdown documents into web pages available at the links below. Analyses are organized by the empirical dataset was used for reference. Details about where to download the empirical data are in the preprocessing page for each dataset.
- 10x Differentiating iPSCs (floor plate progenitors and dopaminergic neurons)
- SmartSeq2 iPSCs from HipSci (multiple batches)
- 10x Fibroblasts (with and without bleomycin to induce fibrosis)
- Example use cases
- Other analyses
eQTL mapping was done using the best practices as described in Cuomo, Alveri, Azodi, et. al. Snakemake was used to automate that workflow.
Reference Data
Reference VCF and GFF files for chromosome 22 were downloaded and processed as follows.
Reference VCF
# Download
wget http://hgdownload.cse.ucsc.edu/gbdb/hg19/1000Genomes/phase3/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
mv ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz chr22.vcf.gz
# Filter
conda activate plink
plink --vcf chr22.vcf.gz --biallelic-only --snps-only --geno 0 --maf 0.05 --hwe 0.00001 --indep-pairwise 1600 5 0.75 --keep keep_samples.txt --out chr22.filt --recode
plink --vcf chr22.vcf.gz --extract chr22.filt.prune.in --keep keep_samples.txt --recode vcf --out chr22.filtered
# Output: chr22.filtered.vcf**Reference GFF
## Download
wget http://ftp.ensembl.org/pub/release-99/gff3/homo_sapiens/Homo_sapiens.GRCh38.99.chromosome.22.gff3.gz
## Filter
gunzip Homo_sapiens.GRCh38.99.chromosome.22.gff3.gz
awk '$3 == "gene"' Homo_sapiens.GRCh38.99.chromosome.22.gff3 > Homo_sapiens.GRCh38.99.chromosome.22.genes.gff3
mv Homo_sapiens.GRCh38.99.chromosome.22.genes.gff3 chr22.genes.gff3
# Output: chr22.genes.gff3With the data downloaded and organised as above, you will be able to reproduce the analyses presented in the RMarkdown files linked to above and, if desired, even run the whole analysis pipeline.
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
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R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.1)
Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.1)
remotes 2.4.1 2021-09-29 [1] CRAN (R 4.1.1)
rlang 0.4.12 2021-10-18 [1] CRAN (R 4.0.4)
rmarkdown 2.11 2021-09-14 [1] CRAN (R 4.1.1)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.1)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.1)
sass 0.4.0 2021-05-12 [1] CRAN (R 4.1.1)
sessioninfo 1.2.1 2021-11-02 [1] CRAN (R 4.1.1)
stringi 1.7.5 2021-10-04 [1] CRAN (R 4.0.4)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.1)
testthat 3.1.0 2021-10-04 [1] CRAN (R 4.1.1)
tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.1)
usethis 2.1.3 2021-10-27 [1] CRAN (R 4.1.1)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.0.4)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.1)
whisker 0.4 2019-08-28 [1] CRAN (R 4.1.1)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.1)
workflowr 1.6.2 2020-04-30 [1] CRAN (R 4.1.1)
xfun 0.28 2021-11-04 [1] CRAN (R 4.1.1)
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.1)
[1] /mnt/mcfiles/cazodi/R/x86_64-pc-linux-gnu-library/4.1
[2] /opt/R/4.1.1/lib/R/library
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