Home

Last updated: 2020-07-02

Checks: 2 0

Knit directory: neural_scRNAseq/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). 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: a9389d9

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 a9389d9. 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:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    ._.DS_Store
    Ignored:    ._Rplots.pdf
    Ignored:    .__workflowr.yml
    Ignored:    ._neural_scRNAseq.Rproj
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/.Rhistory
    Ignored:    analysis/._.DS_Store
    Ignored:    analysis/._01-preprocessing.Rmd
    Ignored:    analysis/._01-preprocessing.html
    Ignored:    analysis/._02.1-SampleQC.Rmd
    Ignored:    analysis/._03-filtering.Rmd
    Ignored:    analysis/._04-clustering.Rmd
    Ignored:    analysis/._04-clustering.knit.md
    Ignored:    analysis/._04.1-cell_cycle.Rmd
    Ignored:    analysis/._05-annotation.Rmd
    Ignored:    analysis/._NSC-1-clustering.Rmd
    Ignored:    analysis/._NSC-2-annotation.Rmd
    Ignored:    analysis/.__site.yml
    Ignored:    analysis/._additional_filtering.Rmd
    Ignored:    analysis/._additional_filtering_clustering.Rmd
    Ignored:    analysis/._index.Rmd
    Ignored:    analysis/01-preprocessing_cache/
    Ignored:    analysis/02-1-SampleQC_cache/
    Ignored:    analysis/02-quality_control_cache/
    Ignored:    analysis/02.1-SampleQC_cache/
    Ignored:    analysis/03-filtering_cache/
    Ignored:    analysis/04-clustering_cache/
    Ignored:    analysis/04.1-cell_cycle_cache/
    Ignored:    analysis/05-annotation_cache/
    Ignored:    analysis/NSC-1-clustering_cache/
    Ignored:    analysis/NSC-2-annotation_cache/
    Ignored:    analysis/additional_filtering_cache/
    Ignored:    analysis/additional_filtering_clustering_cache/
    Ignored:    analysis/sample5_QC_cache/
    Ignored:    data/.DS_Store
    Ignored:    data/._.DS_Store
    Ignored:    data/._.smbdeleteAAA17ed8b4b
    Ignored:    data/._known_NSC_markers.R
    Ignored:    data/._known_cell_type_markers.R
    Ignored:    data/._metadata.csv
    Ignored:    data/data_sushi/
    Ignored:    data/filtered_feature_matrices/
    Ignored:    output/.DS_Store
    Ignored:    output/._.DS_Store
    Ignored:    output/NSC_1_clustering.rds
    Ignored:    output/additional_filtering.rds
    Ignored:    output/figures/
    Ignored:    output/sce_01_preprocessing.rds
    Ignored:    output/sce_02_quality_control.rds
    Ignored:    output/sce_03_filtering.rds
    Ignored:    output/sce_preprocessing.rds
    Ignored:    output/so_04_1_cell_cycle.rds
    Ignored:    output/so_04_clustering.rds
    Ignored:    output/so_additional_filtering_clustering.rds

Untracked files:
    Untracked:  Rplots.pdf
    Untracked:  analysis/additional_filtering.Rmd
    Untracked:  analysis/additional_filtering_clustering.Rmd
    Untracked:  analysis/sample5_QC.Rmd
    Untracked:  analysis/tabsets.Rmd
    Untracked:  scripts/

Unstaged changes:
    Modified:   analysis/_site.yml

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	6d0742b	khembach	2020-07-02	wflow_publish(c(“analysis/NSC-1-clustering.Rmd”, “analysis/NSC-2-annotation.Rmd”,
html	06330b1	khembach	2020-06-22	Build site.
Rmd	f349423	khembach	2020-06-21	regress out number of UMIs and perc mitochondrial features; cyclone
html	a4d0e04	khembach	2020-05-29	Build site.
Rmd	97d5a52	khembach	2020-05-29	cluster analysis
html	a94efaa	khembach	2020-05-29	Build site.
Rmd	7f5c1f8	khembach	2020-05-29	dimension reduction and clustering
html	6d822af	khembach	2020-05-28	Build site.
Rmd	a7ced59	khembach	2020-05-28	cell and gene filtering
html	1230f08	khembach	2020-05-27	Build site.
Rmd	6be1a5a	khembach	2020-05-27	rebuild without cache and SampleQC report
html	bb957e8	khembach	2020-05-26	Build site.
Rmd	4acc3c4	khembach	2020-05-26	Link to preprocessing and QC
html	16fe492	khembach	2020-05-22	Build site.
Rmd	e4c9cd1	khembach	2020-05-22	Start workflowr project.