├── .gitignore ├── LICENSE ├── README.md ├── config ├── config.yaml ├── prior_cats.json └── slurm │ ├── CookieCutter.py │ ├── config.yaml │ ├── settings.json │ ├── slurm-jobscript.sh │ ├── slurm-sidecar.py │ ├── slurm-status.py │ ├── slurm-submit.py │ └── slurm_utils.py ├── docs ├── dbs.md ├── dts.md └── mth.md └── workflow ├── Snakefile ├── envs ├── celloracle.def ├── crema.def ├── dictys.def ├── dictys.yaml ├── directnet.def ├── figr.def ├── granie.def ├── gretabench.def ├── hummus.def ├── inferelator.def ├── pando.def ├── scdori.yaml ├── scenicplus.def ├── scgpt.yaml └── scmtni.def ├── rules ├── anl │ ├── dbs.smk │ ├── dts.smk │ ├── metrics │ │ ├── genom.smk │ │ ├── mech.smk │ │ ├── pred.smk │ │ ├── prior.smk │ │ ├── simul.smk │ │ └── utils.smk │ ├── pair.smk │ ├── stab.smk │ ├── topo.smk │ └── tss.smk ├── dbs │ ├── c2g.smk │ ├── cre.smk │ ├── gen.smk │ ├── gst.smk │ ├── ont.smk │ ├── prt.smk │ ├── sim.smk │ ├── tfb.smk │ ├── tfm.smk │ ├── tfp.smk │ └── tss.smk ├── dts │ ├── brain.smk │ ├── breast.smk │ ├── embryo.smk │ ├── eye.smk │ ├── fakepair.smk │ ├── general.smk │ ├── heart.smk │ ├── kidney.smk │ ├── lung.smk │ ├── mouse.smk │ ├── pbmc10k.smk │ ├── pitunpair.smk │ ├── pitupair.smk │ ├── reprofibro.smk │ └── skin.smk ├── img │ └── img.smk ├── mth │ ├── celloracle.smk │ ├── correlation.smk │ ├── crema.smk │ ├── dictys.smk │ ├── directnet.smk │ ├── figr.smk │ ├── granie.smk │ ├── grn.smk │ ├── hummus.smk │ ├── inferelator.smk │ ├── pando.smk │ ├── random.smk │ ├── scdori.smk │ ├── scenic.smk │ ├── scenicplus.smk │ ├── scgpt.smk │ └── scmtni.smk └── plt │ ├── comb.smk │ ├── dbs.smk │ ├── eval.smk │ ├── figs.smk │ ├── pair.smk │ ├── simul.smk │ └── stab.smk └── scripts ├── anl ├── dbs │ ├── HPA_plt.py │ ├── ocoef.py │ ├── stats.py │ └── terms.py ├── dts │ └── qcstats.py ├── metrics │ ├── aggregate.py │ ├── genom │ │ └── gnm.py │ ├── mech │ │ ├── prt.py │ │ ├── sim.py │ │ ├── tfa.py │ │ └── tfm.py │ ├── pred │ │ ├── gsets.py │ │ └── omics.py │ ├── prior │ │ ├── grn.py │ │ ├── tfm.py │ │ └── tfp.py │ ├── simul │ │ └── simul.py │ ├── test.py │ └── utils.py ├── pair │ ├── fake_stats.py │ ├── pairsim.py │ ├── real_cors.py │ └── realqc.py ├── stab │ ├── ovsd.py │ ├── run_stab.py │ └── seeds.py ├── topo │ ├── fvsd.py │ ├── inter.py │ ├── run_pair_sim.py │ └── simul.py ├── tss │ ├── dist.py │ └── gocoef.py └── utils.py ├── dbs ├── c2g │ ├── eqtlcat_gene.py │ └── eqtlcat_smpl.py ├── cre │ ├── gwascatalogue.py │ ├── promoters.R │ └── promoters_mm10.R ├── gen │ ├── genome │ │ ├── celloracle.py │ │ └── celloracle_mm10.py │ ├── gid │ │ └── ensmbl.R │ ├── motif │ │ └── fix_dictys_caps.py │ ├── pid │ │ └── uniprot.R │ ├── tfs │ │ └── lambert_from_ensembl.py │ └── tss │ │ ├── celloracle.py │ │ ├── dictys.py │ │ ├── directnet.py │ │ ├── figr.R │ │ ├── granie.R │ │ ├── hummus.R │ │ ├── pando.R │ │ └── scenicplus.py ├── gst │ └── pways.py ├── ont │ └── bto.py ├── sim │ └── pre.py ├── tfb │ ├── aggregate.py │ ├── chipatlas_meta.py │ ├── chipatlas_tf.py │ ├── remap2022_meta.py │ ├── remap2022_meta_mm10.py │ ├── remap2022_raw.py │ ├── remap2022_raw_mm10.py │ └── unibind_raw.py ├── tfm │ └── hpa.py └── tfp │ ├── europmc.py │ ├── europmc_raw.py │ └── intact.py ├── dts ├── brain │ ├── brain.py │ └── prc_annot.py ├── breast │ ├── annot.py │ ├── breast.py │ ├── compress_sample.sh │ ├── filter_sample.awk │ └── write_sample.sh ├── callpeaks.py ├── callpeaks_mm10.py ├── embryo │ ├── embryo.py │ └── prcrna.py ├── extract_case.py ├── eye │ ├── eye.py │ ├── prcrna.py │ └── split.py ├── fakepair │ ├── coembedd.R │ ├── fakepair.py │ └── paircells.R ├── format_frags.sh ├── heart │ ├── heart.py │ └── heart_annot.py ├── kidney │ ├── annot.py │ └── kidney.py ├── lung │ ├── annot.py │ └── lung.py ├── mouse │ ├── filter_merge.py │ ├── h5_to_h5ad.py │ ├── mouse.py │ └── rds_to_annot.R ├── pbmc10k │ ├── pbmc10k.py │ └── prc_annot.py ├── pitunpair │ ├── coembedd.R │ ├── paircells.R │ └── pitunpair.py ├── pitupair │ └── pitupair.py ├── reprofibro │ ├── prc_annot.py │ └── reprofibro.py └── skin │ ├── prcrna.py │ └── skin.py ├── mth ├── celloracle │ ├── mdl.py │ ├── p2g.R │ ├── p2g.py │ ├── pre.py │ ├── src.R │ ├── src.py │ ├── tfb.py │ └── tfb_mm10.py ├── correlation.py ├── crema │ ├── get_inserts.py │ └── src.R ├── dictys │ ├── before_mdl.py │ ├── extract_data.py │ ├── frag_to_bam.py │ ├── mdl.sh │ ├── p2g.py │ ├── pre.py │ └── tfb.sh ├── directnet │ └── src.R ├── figr │ ├── mdl.R │ ├── p2g.R │ ├── pre.R │ ├── src.R │ └── tfb.R ├── granie │ ├── mdl.R │ ├── p2g.R │ ├── pre.R │ ├── pre.py │ ├── pre_post.py │ ├── src.R │ └── tfb.R ├── grn.py ├── hummus │ ├── add_enhancers.py │ ├── create_layers.py │ └── src.R ├── inferelator │ ├── prior.py │ └── run.py ├── pando │ ├── get_granges.R │ ├── mdl.R │ ├── p2g.R │ ├── pre.R │ ├── pre.py │ ├── src.R │ └── tfb.R ├── prc_prior_grn.py ├── random │ └── grn.py ├── scdori │ ├── config.yaml │ ├── grns_scDORI.py │ ├── pp_scDORI.py │ ├── src.py │ ├── train_scDORI.py │ └── utils.py ├── scenic │ ├── 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