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Last updated: 2018-07-28

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✔ R Markdown file: up-to-date

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✔ Repository version: a3d67a7
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
```
Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    docs/.DS_Store
    Ignored:    docs/images/.DS_Store
    Ignored:    docs/images/.Rapp.history
    Ignored:    output/.DS_Store
    Ignored:    output/.Rapp.history
    Ignored:    output/MASHvFLASHsims/.DS_Store
    Ignored:    output/MASHvFLASHsims/backfit/.DS_Store

Untracked files:
    Untracked:  code/gtex3.R
    Untracked:  output/gtex3mfit.rds
    Untracked:  output/gtex3mrandfit.rds
```
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.

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File	Version	Author	Date	Message
Rmd	a3d67a7	Jason Willwerscheid	2018-07-28	wflow_publish(“analysis/index.Rmd”)
html	76619ea	Jason Willwerscheid	2018-07-22	Build site.
Rmd	30e7d23	Jason Willwerscheid	2018-07-22	wflow_publish(c(“analysis/index.Rmd”,
html	fce2b77	Jason Willwerscheid	2018-07-22	Build site.
Rmd	302143d	Jason Willwerscheid	2018-07-22	wflow_publish(c(“analysis/index.Rmd”, “analysis/about.Rmd”))
html	f4ebd13	Jason Willwerscheid	2018-06-27	Build site.
Rmd	2ce499f	Jason Willwerscheid	2018-06-27	wflow_publish(c(“analysis/about.Rmd”, “analysis/index.Rmd”))
html	a9c6a2d	Jason Willwerscheid	2018-06-26	Build site.
Rmd	e6b255b	Jason Willwerscheid	2018-06-26	wflow_publish(“analysis/index.Rmd”)
html	07d1fc7	Jason Willwerscheid	2018-06-24	Build site.
Rmd	660d4c5	Jason Willwerscheid	2018-06-24	wflow_publish(c(“analysis/index.Rmd”))
html	97fa87c	Jason Willwerscheid	2018-06-24	Build site.
Rmd	42cd89c	Jason Willwerscheid	2018-06-24	wflow_publish(c(“analysis/MASHvFLASHsims2.Rmd”,
html	05ddaac	Jason Willwerscheid	2018-06-18	Build site.
Rmd	59c9e8e	Jason Willwerscheid	2018-06-18	wflow_publish(“analysis/index.Rmd”)
html	c7561ae	Jason Willwerscheid	2018-06-18	Build site.
Rmd	6422a12	Jason Willwerscheid	2018-06-18	wflow_publish(“analysis/index.Rmd”)
html	55504ec	Jason Willwerscheid	2018-06-16	Build site.
Rmd	94b77ff	Jason Willwerscheid	2018-06-16	wflow_publish(“analysis/index.Rmd”)
html	95f1aca	Jason Willwerscheid	2018-06-15	Build site.
Rmd	2052215	Jason Willwerscheid	2018-06-15	wflow_publish(“analysis/index.Rmd”)
html	958fa1e	Jason Willwerscheid	2018-06-11	Build site.
Rmd	99104f2	Jason Willwerscheid	2018-06-11	wflow_publish(“analysis/index.Rmd”)
html	a738d4a	Jason Willwerscheid	2018-06-09	Build site.
Rmd	6e63015	Jason Willwerscheid	2018-06-09	wflow_publish(“analysis/index.Rmd”)
html	53ca12c	Jason Willwerscheid	2018-06-09	initial setup
Rmd	3314e19	Jason Willwerscheid	2018-06-09	Start workflowr project.

Introduction. A vignette.

MASH v FLASH simulation results. Compares FLASH fits to MASH fits to data simulated from both MASH and FLASH models.

MASH v FLASH on GTEx. Compares FLASH to MASH using data from the GTEx project. Results are similar, but FLASH is more conservative.

MASH v FLASH detailed simulation study. Using the “OHL” method, compares the performance of FLASH-pn, FLASH-ash, and MASH in a single simulation setting. FLASH and MASH perform differently on different covariance structures. There is little or no advantage to using ash priors rather than point-normals.

MASH v FLASH detailed GTEx study. Uses an improved workflow to examine differences in MASH and FLASH fits to GTEx data. Particularly strong effects in a single condition might cause MASH to miss smaller effects that are shared among conditions. But FLASH might miss very small effects that are shared across all conditions.

Archived:

A first attempt. Stowed and forgotten.

This reproducible R Markdown analysis was created with workflowr 1.0.1