Enhancer plot

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

.gitignore

@@ -2,15 +2,17 @@
 .snakemake
 ._dag.png
 .DS_Store
-<<<<<<< HEAD
 **/__pycache__/
 *.py[cod]
-=======
 */__pycache__/
->>>>>>> 1384bcec7fd21b92b2dd6e3203d5fc38ff522141
 renv/cellar/
 renv/library/
 renv/local/
 renv/lock/
 renv/python/
 renv/staging/
+<<<<<<< HEAD
+**/*.h5ad
+*data/
+*results/
+

README.md

@@ -8,7 +8,7 @@ This repository contains a [`snakemake`](https://snakemake.readthedocs.io/en/sta
 
 ## Overview:
 
-Below is a DAG showing the rule dependencies in the `snakemake` pipeline. View the [`Snakefile`](https://github.com/settylab/geneTF/blob/main/workflow/Snakefile) to see details on each rule.
+Below is a DAG showing the rule dependencies in the `snakemake` pipeline. View the [`Snakefile`](https://github.com/settylab/atac-metacell-utilites/blob/main/workflow/Snakefile) to see details on each rule.
 
 ![DAG of workflow](./dag.png)
 
@@ -244,9 +244,9 @@ For example, the following will run/re-run the `chromvar` rule and any of the al
 ```
 snakemake --cores 1 chromvar --allowed_rules peak_tf compute_ins_chip prep_chromvar
 ```
-When running this pipeline on an HPC system which uses `lmod` to load software, do not load snakemake as a module - this can cause conflicts where the Python version used by `snakemake` is the one provided by the module, not the `gene-TF` conda environment.
+When running this pipeline on an HPC system which uses `lmod` to load software, do not load snakemake as a module - this can cause conflicts where the Python version used by `snakemake` is the one provided by the module, not the `atac-metacell-utils` conda environment.
 
-To run using the snakemake version installed with `gene-TF`, make sure the `gene-TF` environment is active, then run the pipeline as follows:
+To run using the snakemake version installed with `atac-metacell-utils`, make sure the `atac-metacell-utils` environment is active, then run the pipeline as follows:
 
 ```
 python -m snakemake --cores 1 name-of-rule

config/full-test-config.yaml

@@ -0,0 +1,49 @@
+scripts: "workflow/scripts/"
+output: "full-test-results/"
+logs: "full-test-logs/"
+interactive_clean: True
+
+renv_loc: "/home/cjordan2/R/x86_64-pc-linux-gnu-library/4.1.0" # <path/to/user/R/library>
+
+anndata:
+    atac: "/fh/fast/setty_m/user/cjordan2/repositories/density-analysis/data/bm_atac_meta_ad.h5ad" #"/fh/fast/setty_m/user/cjordan2/repositories/geneTF/data/test_atac_meta_ad.h5ad"  #<<path/to/SEACell/ATAC/AnnData/here>
+    rna: "/fh/fast/setty_m/user/cjordan2/repositories/density-analysis/data/bm_rna_meta_ad.h5ad" #tcell_dep_rna_w_SEACells_meta.h5ad" #"/fh/fast/setty_m/user/cjordan2/repositories/geneTF/data/test_rna_meta_ad.h5ad" #<path/to/SEACell/RNA/AnnData/here>
+    sc_atac: "/fh/fast/setty_m/user/cjordan2/repositories/density-analysis/data/snapshot_ads/bm_atac_ad.h5ad" #"/fh/fast/setty_m/user/cjordan2/repositories/geneTF/data/test_atac_ad.h5ad" 
+    sc_rna: "/fh/fast/setty_m/user/cjordan2/repositories/density-analysis/data/snapshot_ads/bm_rna_ad.h5ad" #"/fh/fast/setty_m/user/cjordan2/repositories/geneTF/data/test_rna_ad.h5ad" 
+    # documenting what label was used to create the SEACells AnnData - also used for differential accessibility
+    SEACell_label: "SEACell"
+peaks:
+    width: 150
+    genome: "hg38"
+    meme_file: "data/cis-bp-tf-information.meme"
+
+ins_chip:
+    # set verbose to "--verbose" for True
+    verbose: ""
+    min_chip_score: 0.15
+    min_peak_hits: 30
+
+gene_peak_corr_config:
+    # set test_set to "--test_set" for True
+    n_jobs: 1
+    test_set: ""
+    n_genes: 20
+
+gene_peak_corr_cutoffs:
+    min_corr: 0.0
+    max_pval: 0.1
+    min_peaks: 2
+
+diff_acc:
+    to_compare: "EryPre1,proB/Mono,proB/EryPre1,HSC/Mono,HSC"
+    group_variable: "celltype_combined"
+
+peak_selection:
+    target: ["Bcells","proB"]
+    start: "HSC"
+    reference: 
+         Ery: "EryPre1"
+         Mono: "Mono"
+    min_logFC: -0.25
+    max_logFC: 0.25
+