Last updated: 2021-12-17

Checks: 2 0

Knit directory: sct2_revision/

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: 8afc486

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 8afc486. 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:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    data/raw_data/
    Ignored:    data/rds_filtered/
    Ignored:    data/rds_raw/
    Ignored:    data/sampled_counts/
    Ignored:    output/snakemake_output/

Untracked files:
    Untracked:  code/02_run_seurat_noclip.R
    Untracked:  code/07AA_deseq2_muscat_simulate.R
    Untracked:  code/07A_muscat_simulate.R
    Untracked:  code/07A_simulate_muscat.R
    Untracked:  code/07BB_deseq2_muscat_process.R
    Untracked:  code/07B_muscat_process.R
    Untracked:  code/07B_process_muscat.R
    Untracked:  code/08_run_presto.R
    Untracked:  code/17A_HEK_SS3_dropseq.Rmd
    Untracked:  code/17A_HEK_SS3_dropseq_files/
    Untracked:  code/17C_HEK_Quartzeseq2_dropseq.Rmd
    Untracked:  code/17C_HEK_Quartzeseq2_dropseq_files/
    Untracked:  code/17_HEK_SS3_ChromiumV3.Rmd
    Untracked:  code/17_HEK_SS3_ChromiumV3.nb.html
    Untracked:  code/17_HEK_SS3_ChromiumV3_files/
    Untracked:  code/AA_process_muscat.R
    Untracked:  code/BB_process_muscat.R
    Untracked:  code/DD_simulate_muscat.R
    Untracked:  code/EE_simulate_muscat.R
    Untracked:  code/XX_process_muscat.R
    Untracked:  code/XX_simulate_muscat.R
    Untracked:  code/YY_simulate_muscat.R
    Untracked:  code/ZZ_simulate_muscat.R
    Untracked:  code/kang_muscat.R
    Untracked:  code/prep_sce.R
    Untracked:  code/prep_sce_ss3_dropseq.R
    Untracked:  data/azimuth_predictions/
    Untracked:  junk/
    Untracked:  mamba_update_changes.txt
    Untracked:  output/11C_VST/
    Untracked:  output/AAmuscat_simulated/
    Untracked:  output/BBmuscat_simulated/
    Untracked:  output/CCmuscat_simulated/
    Untracked:  output/CD4_NK_downsampling_DE.rds
    Untracked:  output/DDmuscat_simulated/
    Untracked:  output/EEmuscat_simulated/
    Untracked:  output/KANGmuscat_simulated/
    Untracked:  output/NK_downsampling/
    Untracked:  output/XXmuscat_simulated/
    Untracked:  output/YYmuscat_simulated/
    Untracked:  output/ZZmuscat_simulated/
    Untracked:  output/figures/
    Untracked:  output/kang_prepsce.rds
    Untracked:  output/muscat_simulated/
    Untracked:  output/muscat_simulation/
    Untracked:  output/seu_sct2_sim.rds
    Untracked:  output/simulation_HEK_QuartzSeq2_Dropseq_downsampling/
    Untracked:  output/simulation_HEK_SS3_ChromiumV3_downsampling/
    Untracked:  output/simulation_HEK_SS3_Dropseq_downsampling/
    Untracked:  output/simulation_HEK_downsampling/
    Untracked:  output/simulation_NK_downsampling/
    Untracked:  output/ss3_dropseq_prepsim.rds
    Untracked:  output/tables/
    Untracked:  output/vargenes/
    Untracked:  snakemake/.snakemake/
    Untracked:  snakemake/Snakefile_noclip.smk
    Untracked:  snakemake/Snakefile_presto.smk
    Untracked:  snakemake/cluster.yaml
    Untracked:  snakemake/install_glm.R
    Untracked:  snakemake/jobscript.sh
    Untracked:  snakemake/jobscript_ncells.sh
    Untracked:  snakemake/local_run_downsampling.sh
    Untracked:  snakemake/local_run_glm.sh
    Untracked:  snakemake/local_run_ncells.sh
    Untracked:  snakemake/local_run_noclip.sh
    Untracked:  snakemake/local_run_presto.sh
    Untracked:  snakemake/local_run_time.sh
    Untracked:  snakemake/run_glm.sh
    Untracked:  snakemake/run_ncells.sh
    Untracked:  snakemake/sct2_revision_env.yml
    Untracked:  temp_figures/

Unstaged changes:
    Deleted:    analysis/04_PBMC68k.Rmd
    Modified:   code/02_run_seurat.R
    Modified:   code/03_run_vst2_downsample.R
    Modified:   code/04_run_vst_ncells.R
    Modified:   code/06_run_sct.R
    Modified:   data/datasets.csv
    Modified:   snakemake/Snakefile_downsampling.smk
    Modified:   snakemake/Snakefile_glm_seurat.smk
    Modified:   snakemake/Snakefile_metacell.smk

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/license.Rmd) and HTML (docs/license.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 d736ec8 Saket Choudhary 2021-07-07 Build site.
html 400797a Saket Choudhary 2021-07-06 workflowr::wflow_git_commit(all = TRUE)
Rmd ccb0fb4 Saket Choudhary 2021-07-06 workflowr::wflow_git_commit(all = TRUE)
Rmd e0b7c2c Saket Choudhary 2021-07-06 Start workflowr project.

BSD 2-Clause License

Copyright (c) 2021, Saket Choudhary All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.