LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
SnakeHichipTF.egg-info/PKG-INFO
SnakeHichipTF.egg-info/SOURCES.txt
SnakeHichipTF.egg-info/dependency_links.txt
SnakeHichipTF.egg-info/entry_points.txt
SnakeHichipTF.egg-info/requires.txt
SnakeHichipTF.egg-info/top_level.txt
snakehichiptf/_version.py
snakehichiptf/cli.py
snakehichiptf/data/example_data/Human_MiddleFrontalGyrus1_unknown_WT_unknown_ATAC_standard.filtered.bam
snakehichiptf/data/example_data/Human_MiddleFrontalGyrus1_unknown_WT_unknown_HiChIP_standard_mergedSRR_R1.fastq.gz
snakehichiptf/data/example_data/Human_MiddleFrontalGyrus1_unknown_WT_unknown_HiChIP_standard_mergedSRR_R2.fastq.gz
snakehichiptf/data/example_data/Human_MiddleFrontalGyrus2_unknown_WT_unknown_HiChIP_standard_mergedSRR_R1.fastq.gz
snakehichiptf/data/example_data/Human_MiddleFrontalGyrus2_unknown_WT_unknown_HiChIP_standard_mergedSRR_R2.fastq.gz
snakehichiptf/data/example_data/Human_SubstantiaNigra1_unknown_WT_unknown_HiChIP_standard_mergedSRR_R1.fastq.gz
snakehichiptf/data/example_data/Human_SubstantiaNigra1_unknown_WT_unknown_HiChIP_standard_mergedSRR_R2.fastq.gz
snakehichiptf/data/example_data/Human_SubstantiaNigra2_unknown_WT_unknown_HiChIP_standard_mergedSRR_R1.fastq.gz
snakehichiptf/data/example_data/Human_SubstantiaNigra2_unknown_WT_unknown_HiChIP_standard_mergedSRR_R2.fastq.gz
snakehichiptf/data/example_data/hg38.chr22.fa
snakehichiptf/data/example_data/samplesheet_SubstantiaNigra_vs_MiddleFrontalGyrus.tsv
snakehichiptf/docs/Diffhichip.md
snakehichiptf/docs/Genomesetup.md
snakehichiptf/docs/Snakehichip.md
snakehichiptf/docs/TFscprinter.md
snakehichiptf/docs/TFtobias.md
snakehichiptf/docs/overview.png
snakehichiptf/organisms/all_motifs.txt
snakehichiptf/organisms/basic.txt
snakehichiptf/rules/Diffhichip.Snakefile
snakehichiptf/rules/Genomesetup.Snakefile
snakehichiptf/rules/Snakehichip.Snakefile
snakehichiptf/rules/TFscprinter.Snakefile
snakehichiptf/rules/TFtobias.Snakefile
snakehichiptf/rules/envs/basic.yaml
snakehichiptf/rules/envs/cooler.yaml
snakehichiptf/rules/envs/deeptools.yaml
snakehichiptf/rules/envs/diffloop.yaml
snakehichiptf/rules/envs/fithichip.yaml
snakehichiptf/rules/envs/genomefeature.yaml
snakehichiptf/rules/envs/hicdc.yaml
snakehichiptf/rules/envs/hicexplorer.yaml
snakehichiptf/rules/envs/hichipper.yaml
snakehichiptf/rules/envs/hicpro.yaml
snakehichiptf/rules/envs/maps.yaml
snakehichiptf/rules/envs/mapsrun.yaml
snakehichiptf/rules/envs/r.yaml
snakehichiptf/rules/envs/samtools.yaml
snakehichiptf/rules/envs/scprinter_gpu.yaml
snakehichiptf/rules/envs/tobias.yaml
snakehichiptf/scripts/MAPS.py
snakehichiptf/scripts/MAPS_peak_formatting.r
snakehichiptf/scripts/MAPS_regression_and_peak_caller.r
snakehichiptf/scripts/chr2_scprinter_main.py
snakehichiptf/scripts/feather_filter_all.py
snakehichiptf/scripts/feather_filter_chr.py
snakehichiptf/scripts/feather_filter_chr_hicpro.py
snakehichiptf/scripts/feather_split_all.py
snakehichiptf/scripts/feather_split_rongxin.py
snakehichiptf/scripts/feature_frag2bin.py
snakehichiptf/scripts/generate_site_positions_yq.py
snakehichiptf/scripts/hicdc_differential_interactions.R
snakehichiptf/scripts/hicdc_genomefeature.R
snakehichiptf/scripts/hicdc_significant_interactions.R
snakehichiptf/scripts/hichipper.diffloop_differential_analysis.R
snakehichiptf/scripts/hichipper.diffloop_work.R
snakehichiptf/scripts/logger.py
snakehichiptf/scripts/make_maps_runfile.py
snakehichiptf/scripts/merge_map.py
snakehichiptf/scripts/overlaps_gr1.tsv
snakehichiptf/scripts/overlaps_gr2.tsv
snakehichiptf/scripts/plot_footprints_scprinter_standalone.py
snakehichiptf/scripts/qcReport_make.Rmd
snakehichiptf/scripts/qc_all.R
snakehichiptf/scripts/qc_hichip_barplot.R
snakehichiptf/scripts/qc_hichip_quantiles.py
snakehichiptf/scripts/qc_plot_quantiles.R
snakehichiptf/scripts/restriction_cut_multipleenzyme.py
snakehichiptf/scripts/scprinter_main.py
snakehichiptf/scripts/singlecell_scprinter_main.py
snakehichiptf/scripts/__pycache__/feather_filter_chr.cpython-312.pyc
snakehichiptf/scripts/__pycache__/feather_filter_chr.cpython-36.pyc
snakehichiptf/scripts/__pycache__/feather_filter_chr.cpython-37.pyc
snakehichiptf/scripts/__pycache__/feather_filter_chr.cpython-38.pyc
snakehichiptf/scripts/__pycache__/feather_split_rongxin.cpython-312.pyc
snakehichiptf/scripts/__pycache__/feather_split_rongxin.cpython-36.pyc
snakehichiptf/scripts/__pycache__/feather_split_rongxin.cpython-37.pyc
snakehichiptf/scripts/__pycache__/feather_split_rongxin.cpython-38.pyc
snakehichiptf/scripts/__pycache__/logger.cpython-312.pyc
snakehichiptf/scripts/__pycache__/logger.cpython-36.pyc
snakehichiptf/scripts/__pycache__/logger.cpython-37.pyc
snakehichiptf/scripts/__pycache__/logger.cpython-38.pyc
snakehichiptf/scripts/fithichip/BiasCalc.r
snakehichiptf/scripts/fithichip/CombineNearbyInteraction.py
snakehichiptf/scripts/fithichip/CombineREFragMappGC.r
snakehichiptf/scripts/fithichip/ContactCountDistr.r
snakehichiptf/scripts/fithichip/ContactMatDiffRes.sh
snakehichiptf/scripts/fithichip/CoverageBin.py
snakehichiptf/scripts/fithichip/CoverageBin.r
snakehichiptf/scripts/fithichip/CreateBinMatrixFromBed.r
snakehichiptf/scripts/fithichip/DiffAnalysisHiChIP.r
snakehichiptf/scripts/fithichip/Distance_vs_CC.r
snakehichiptf/scripts/fithichip/Extract_contactMat_HiC.py
snakehichiptf/scripts/fithichip/Filt_Loop_DistThr.r
snakehichiptf/scripts/fithichip/FitHiC_SigInt.r
snakehichiptf/scripts/fithichip/HiC_Simulate_by_ChIP_Coverage.r
snakehichiptf/scripts/fithichip/Interaction.r
snakehichiptf/scripts/fithichip/InteractionHicPro.r
snakehichiptf/scripts/fithichip/InteractionPlots.r
snakehichiptf/scripts/fithichip/Interaction_Sort_Genomic_Distance.r
snakehichiptf/scripts/fithichip/MergeBAMInferPeak.sh
snakehichiptf/scripts/fithichip/PackageTest.r
snakehichiptf/scripts/fithichip/PeakInferHiChIP.sh
snakehichiptf/scripts/fithichip/PlotGenomeBins.r
snakehichiptf/scripts/fithichip/Process_contactMat_HiC.py
snakehichiptf/scripts/fithichip/Significance_Features.r
snakehichiptf/scripts/fithichip/SummaryFitHiChIP.sh
snakehichiptf/scripts/fithichip/result_summary.r
snakehichiptf/scripts/fithichip/scripts/hichip_peak_call_script.sh
snakehichiptf/scripts/fithichip/scripts/sample_script.sh
snakehichiptf/scripts/hicpro-3.1.0/Makefile
snakehichiptf/scripts/hicpro-3.1.0/config-system.txt
snakehichiptf/scripts/hicpro-3.1.0/bin/HiC-Pro
snakehichiptf/scripts/hicpro-3.1.0/bin/utils/digest_genome.py
snakehichiptf/scripts/hicpro-3.1.0/bin/utils/extract_snps.py
snakehichiptf/scripts/hicpro-3.1.0/bin/utils/hicpro2fithic.py
snakehichiptf/scripts/hicpro-3.1.0/bin/utils/hicpro2higlass.sh
snakehichiptf/scripts/hicpro-3.1.0/bin/utils/hicpro2juicebox.sh
snakehichiptf/scripts/hicpro-3.1.0/bin/utils/make_viewpoints.py
snakehichiptf/scripts/hicpro-3.1.0/bin/utils/sparseToDense.py
snakehichiptf/scripts/hicpro-3.1.0/bin/utils/split_reads.py
snakehichiptf/scripts/hicpro-3.1.0/bin/utils/split_sparse.py
snakehichiptf/scripts/hicpro-3.1.0/scripts/Makefile
snakehichiptf/scripts/hicpro-3.1.0/scripts/bowtie_combine.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/bowtie_pairing.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/bowtie_wrap.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/build_matrix
snakehichiptf/scripts/hicpro-3.1.0/scripts/build_raw_maps.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/cutsite_trimming
snakehichiptf/scripts/hicpro-3.1.0/scripts/hic.inc.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/ice
snakehichiptf/scripts/hicpro-3.1.0/scripts/ice_norm.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/make_lsf_script.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/make_plots.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/make_sge_script.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/make_slurm_script.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/make_torque_script.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/mapped_2hic_dnase.py
snakehichiptf/scripts/hicpro-3.1.0/scripts/mapped_2hic_fragments.py
snakehichiptf/scripts/hicpro-3.1.0/scripts/mapped_2hic_fragments.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/mapping_stat.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/markAllelicStatus.py
snakehichiptf/scripts/hicpro-3.1.0/scripts/mergeSAM.py
snakehichiptf/scripts/hicpro-3.1.0/scripts/merge_statfiles.py
snakehichiptf/scripts/hicpro-3.1.0/scripts/merge_stats.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/merge_valid_interactions.sh
snakehichiptf/scripts/hicpro-3.1.0/scripts/onTarget.py
snakehichiptf/scripts/hicpro-3.1.0/scripts/plot_hic_contacts.R
snakehichiptf/scripts/hicpro-3.1.0/scripts/plot_hic_fragment.R
snakehichiptf/scripts/hicpro-3.1.0/scripts/plot_mapping_portion.R
snakehichiptf/scripts/hicpro-3.1.0/scripts/plot_pairing_portion.R
snakehichiptf/scripts/hicpro-3.1.0/scripts/split_valid_interactions.py
snakehichiptf/ui/__init__.py
snakehichiptf/ui/launch.py
snakehichiptf/ui/stl_app.py
snakehichiptf/workflows/Diffhichip.py
snakehichiptf/workflows/Genomesetup.py
snakehichiptf/workflows/Snakehichip.py
snakehichiptf/workflows/TFscprinter.py
snakehichiptf/workflows/TFtobias.py
snakehichiptf/workflows/__init__.py