Last updated: 2024-01-30

Checks: 2 0

Knit directory: dgrp-starve/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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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 6e5294b. 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:    .snakemake/
    Ignored:    code/methodComp/bglr/err-bglr-f.5381.err
    Ignored:    code/methodComp/bglr/err-bglr-m.5382.err
    Ignored:    code/methodComp/m/meth-m.4676.err
    Ignored:    code/methodComp/m/meth-m.4685.err
    Ignored:    code/methodComp/method-f.4751.out
    Ignored:    data/fb/
    Ignored:    data/snake/
    Ignored:    snake/.snakemake/
    Ignored:    snake/GOfile.yaml
    Ignored:    snake/
    Ignored:    snake/code/bayesC/
    Ignored:    snake/code/misc/
    Ignored:    snake/customL.Rds
    Ignored:    snake/data/
    Ignored:    snake/datafile.yaml
    Ignored:    snake/dgrp.yaml
    Ignored:    snake/fig/
    Ignored:    snake/fullGO.yaml
    Ignored:    snake/gofig.yaml
    Ignored:    snake/guide/
    Ignored:    snake/logs/
    Ignored:    snake/pbs_smake.pbs
    Ignored:    snake/pbsmake.sbatch
    Ignored:    snake/slurm/
    Ignored:    snake/smake.sbatch
    Ignored:    snake/snubnose.sbatch
    Ignored:    snake/zz_lost/
    Ignored:    zz_lost/

Untracked files:
    Untracked:  analysis/allotter.R
    Untracked:  analysis/old_index.Rmd.Rmd
    Untracked:  analysis/sparseComp.Rmd
    Untracked:  forester.R
    Untracked:  malegofind.R
    Untracked:  moarnotes.R
    Untracked:  pippinRMDbackup.R
    Untracked:  snake/code/binner.R
    Untracked:  snake/code/combine_GO.R
    Untracked:  snake/code/dataFinGO.R
    Untracked:  snake/code/datafile.yaml
    Untracked:  snake/code/filterNcombine_GO.R
    Untracked:  snake/code/filter_GO.R
    Untracked:  snake/code/go/
    Untracked:  snake/code/idTEMP.R
    Untracked:  snake/code/imstuff.R
    Untracked:  snake/code/method/bayesHome.R
    Untracked:  snake/code/method/multiplotGO.Rmd
    Untracked:  snake/code/scheming.R
    Untracked:  snake/code/scripts/
    Untracked:  snake/code/srfile.yaml
    Untracked:  teno.R

Unstaged changes:
    Modified:   analysis/Method/BayesC.Rmd
    Modified:   analysis/bigGO.Rmd
    Modified:   analysis/enrich.Rmd
    Modified:   snake/code/method/bayesGO.R
    Modified:   snake/code/method/goFish.R
    Modified:   snake/code/method/varbvs.R
    Modified:   snake/temp.txt

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
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Rmd ab7c98c nklimko 2024-01-30 wflow_publish(“analysis/index.Rmd”)
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Rmd 64bb8ec nklimko 2023-07-11 fix index
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Rmd 19e444b nklimko 2023-05-30 wflow_publish(“analysis/index.Rmd”)
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Rmd 951799a nklimko 2023-01-08 wflow_publish("analysis/*")
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Rmd 3a282f1 nklimko 2022-11-11 wflow_publish("analysis/*")
html 0ce7be4 nklimko 2022-11-10 code sync
Rmd b90e540 nklimko 2022-11-09 wflow_git_commit(all = TRUE)
html b90e540 nklimko 2022-11-09 wflow_git_commit(all = TRUE)
html 81037cc nklimko 2022-11-09 html reworking, snp success
html e9314ce nklimko 2022-11-05 wflow_git_commit(all = TRUE)
Rmd 3dab5a8 nklimko 2022-11-01 all files for me
html 3dab5a8 nklimko 2022-11-01 all files for me


GO Enrichment

Sparse Group LASSO