Last updated: 2022-09-16

Checks: 2 0

Knit directory: GSFA_analysis/

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Repository version: 4636518

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Ignored files:
    Ignored:    .Rhistory
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Untracked files:
    Untracked:  Rplots.pdf
    Untracked:  analysis/check_Tcells_datasets.Rmd
    Untracked:  analysis/fscLVM_analysis.Rmd
    Untracked:  analysis/spca_LUHMES_data.Rmd
    Untracked:  analysis/test_seurat.Rmd
    Untracked:  code/gsfa_negctrl_job.sbatch
    Untracked:  code/music_LUHMES_Yifan.R
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    Untracked:  code/run_fscLVM_LUHMES_data.R
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    Untracked:  code/run_music_LUHMES_data_20topics.sbatch
    Untracked:  code/run_sceptre_Tcells_data.sbatch
    Untracked:  code/run_sceptre_Tcells_stimulated_data.sbatch
    Untracked:  code/run_sceptre_Tcells_test_data.sbatch
    Untracked:  code/run_sceptre_Tcells_unstimulated_data.sbatch
    Untracked:  code/run_sceptre_permuted_data.sbatch
    Untracked:  code/run_spca_LUHMES.R
    Untracked:  code/run_spca_TCells.R
    Untracked:  code/run_twostep_clustering_LUHMES_data.sbatch
    Untracked:  code/run_twostep_clustering_Tcells_data.sbatch
    Untracked:  code/run_unguided_gsfa_LUHMES.R
    Untracked:  code/run_unguided_gsfa_LUHMES.sbatch
    Untracked:  code/run_unguided_gsfa_Tcells.R
    Untracked:  code/run_unguided_gsfa_Tcells.sbatch
    Untracked:  code/sceptre_LUHMES_data.R
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Unstaged changes:
    Modified:   analysis/music_LUHMES_data.Rmd
    Modified:   analysis/sceptre_TCells_data.Rmd
    Modified:   analysis/twostep_clustering_LUHMES_data.Rmd
    Modified:   code/run_sceptre_LUHMES_data.R
    Modified:   code/run_sceptre_LUHMES_data.sbatch
    Modified:   code/run_sceptre_LUHMES_permuted_data.R
    Modified:   code/run_sceptre_Tcells_permuted_data.R
    Modified:   code/run_sceptre_cropseq_data.sbatch
    Modified:   code/run_twostep_clustering_LUHMES_data.R
    Modified:   code/sceptre_analysis.R

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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 4636518 kevinlkx 2022-09-16 updated sceptre results
html a70a0ab kevinlkx 2022-09-03 Build site.
Rmd 7e1fd41 kevinlkx 2022-09-03 added link to compare_gsfa_mast_degs.html
html c59abc4 kevinlkx 2022-09-01 Build site.
Rmd 28ad987 kevinlkx 2022-09-01 added link to check_gsfa_targets_degs.html
html 718e0a1 kevinlkx 2022-08-31 Build site.
Rmd 65f1ca8 kevinlkx 2022-08-31 added Distribution of DEGs by expression level bins
html 18a8789 kevinlkx 2022-08-25 Build site.
Rmd 9f7cf17 kevinlkx 2022-08-25 added unguided GSFA results
html 452f1cf kevinlkx 2022-08-11 Build site.
Rmd 6abd5b0 kevinlkx 2022-08-11 added two-step clustering analysis
html 9f790ac kevinlkx 2022-08-01 Build site.
Rmd 86a2b00 kevinlkx 2022-08-01 added GSFA results (without DEGs)
html 36e302e kevinlkx 2022-07-25 Build site.
Rmd c1cf005 kevinlkx 2022-07-25 add music results
html d21bdcb kevinlkx 2022-05-26 Build site.
Rmd ff61938 kevinlkx 2022-05-26 added the tutorial for testing SCEPTRE on example data
html 8a77bd6 kevinlkx 2022-05-26 Build site.
Rmd 3c5828d kevinlkx 2022-05-26 added SCEPTRE analysis for LUHMES and T Cell CROP-seq datasets
Rmd 54fe0bd kevinlkx 2022-05-24 Start workflowr project.

GSFA analysis

SCEPTRE analysis

MUSIC analysis

Two-step clustering analysis

Two-step factor analysis using unguided GSFA

Other analysis