Last updated: 2023-08-08

Checks: 2 0

Knit directory: G000204_duplex/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: 0c24851

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 0c24851. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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:    .Rapp.history
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/cache/
    Ignored:    data/.DS_Store
    Ignored:    scripts/

Untracked files:
    Untracked:  ._.DS_Store
    Untracked:  ._rare-mutation-detection.Rproj
    Untracked:  DOCNAME
    Untracked:  analysis/._.DS_Store
    Untracked:  analysis/._ecoli_spikeins.Rmd
    Untracked:  analysis/calc_nanoseq_metrics.Rmd
    Untracked:  data/._.DS_Store
    Untracked:  data/._metrics.rds
    Untracked:  data/ecoli/
    Untracked:  data/ecoli_k12_metrics.rds
    Untracked:  data/human_mixture_capture_region.bed
    Untracked:  data/human_mixture_refs
    Untracked:  data/human_mixture_vars
    Untracked:  data/metadata/
    Untracked:  data/metrics_efficiency_nossc.rds
    Untracked:  data/metrics_spikeins.rds
    Untracked:  data/mixtures
    Untracked:  data/natasha_anstee_metrics.rds
    Untracked:  data/ref/
    Untracked:  drop_out_rate.pdf
    Untracked:  efficiency.pdf
    Untracked:  prototype_code/
    Untracked:  stats.csv

Unstaged changes:
    Modified:   analysis/model.Rmd

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 (docs/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
Rmd 0c24851 mcmero 2023-08-08 Added human mixture variant analysis
html f90d40a Marek Cmero 2022-08-18 Build site.
html 565d602 Marek Cmero 2022-07-13 Build site.
Rmd 847a8c2 Marek Cmero 2022-07-13 Added variant analysis for E coli spike ins
html 9a639c3 Marek Cmero 2022-07-12 Build site.
Rmd 2ec3680 Marek Cmero 2022-07-12 Added preliminary QC results/metrics from spike-in experiments
html b524238 Marek Cmero 2022-05-26 Build site.
Rmd afd79e5 Marek Cmero 2022-05-26 Added revised model, in silico mixtures redone with 1 supporting read, added input cell estimates
html 491e97d Marek Cmero 2022-05-19 Build site.
Rmd 434e8b9 Marek Cmero 2022-05-19 Added in silico mixtures to navigation
html cc380cc Marek Cmero 2022-05-11 Build site.
Rmd 48b6d2e Marek Cmero 2022-05-11 Added statistical tests with xGen rep 1 outlier removed
html e5b39ad Marek Cmero 2022-03-25 Build site.
Rmd 1926d3d Marek Cmero 2022-03-25 added K12 ecoli metrics
html 859670e Marek Cmero 2022-03-22 Build site.
Rmd ab513a4 Marek Cmero 2022-03-22 Fix multiQC report locations
html 5fd8f9a Marek Cmero 2022-03-10 Build site.
Rmd b257d52 Marek Cmero 2022-03-10 Added MGI vs. Illumina comparison; refactoring ecoli.Rmd code
html e5ed9a7 Marek Cmero 2021-12-15 Build site.
Rmd ed42fa9 Marek Cmero 2021-12-15 Added multiQC reports
html 5a3c6b1 Marek Cmero 2021-12-15 Build site.
html de277d9 Marek Cmero 2021-12-15 Build site.
Rmd e610f97 Marek Cmero 2021-12-15 Added ecoli analysis
html b680ba0 mcmero 2021-09-17 Build site.
Rmd ebb9d74 mcmero 2021-09-17 initial commit
html ebb9d74 mcmero 2021-09-17 initial commit
Rmd c9324ad mcmero 2021-09-16 Start workflowr project.

Nanoseq rare mutation detection