python-scripts/Diffhichip
python-scripts/Genomesetup
python-scripts/Snakehichip
python-scripts/TFscprinter
python-scripts/TFtobias
python-scripts/snakehichiptf
python-scripts/snakehichiptf-ui
site-packages/snakehichiptf-0.1.4.dist-info/INSTALLER
site-packages/snakehichiptf-0.1.4.dist-info/METADATA
site-packages/snakehichiptf-0.1.4.dist-info/RECORD
site-packages/snakehichiptf-0.1.4.dist-info/REQUESTED
site-packages/snakehichiptf-0.1.4.dist-info/WHEEL
site-packages/snakehichiptf-0.1.4.dist-info/direct_url.json
site-packages/snakehichiptf-0.1.4.dist-info/entry_points.txt
site-packages/snakehichiptf-0.1.4.dist-info/licenses/LICENSE
site-packages/snakehichiptf-0.1.4.dist-info/top_level.txt
site-packages/snakehichiptf/_version.py
site-packages/snakehichiptf/cli.py
site-packages/snakehichiptf/data/example_data/Human_MiddleFrontalGyrus1_unknown_WT_unknown_ATAC_standard.filtered.bam
site-packages/snakehichiptf/data/example_data/Human_MiddleFrontalGyrus1_unknown_WT_unknown_HiChIP_standard_mergedSRR_R1.fastq.gz
site-packages/snakehichiptf/data/example_data/Human_MiddleFrontalGyrus1_unknown_WT_unknown_HiChIP_standard_mergedSRR_R2.fastq.gz
site-packages/snakehichiptf/data/example_data/Human_MiddleFrontalGyrus2_unknown_WT_unknown_HiChIP_standard_mergedSRR_R1.fastq.gz
site-packages/snakehichiptf/data/example_data/Human_MiddleFrontalGyrus2_unknown_WT_unknown_HiChIP_standard_mergedSRR_R2.fastq.gz
site-packages/snakehichiptf/data/example_data/Human_SubstantiaNigra1_unknown_WT_unknown_HiChIP_standard_mergedSRR_R1.fastq.gz
site-packages/snakehichiptf/data/example_data/Human_SubstantiaNigra1_unknown_WT_unknown_HiChIP_standard_mergedSRR_R2.fastq.gz
site-packages/snakehichiptf/data/example_data/Human_SubstantiaNigra2_unknown_WT_unknown_HiChIP_standard_mergedSRR_R1.fastq.gz
site-packages/snakehichiptf/data/example_data/Human_SubstantiaNigra2_unknown_WT_unknown_HiChIP_standard_mergedSRR_R2.fastq.gz
site-packages/snakehichiptf/data/example_data/hg38.chr22.fa
site-packages/snakehichiptf/data/example_data/samplesheet_SubstantiaNigra_vs_MiddleFrontalGyrus.tsv
site-packages/snakehichiptf/docs/Diffhichip.md
site-packages/snakehichiptf/docs/Genomesetup.md
site-packages/snakehichiptf/docs/Snakehichip.md
site-packages/snakehichiptf/docs/TFscprinter.md
site-packages/snakehichiptf/docs/TFtobias.md
site-packages/snakehichiptf/docs/overview.png
site-packages/snakehichiptf/organisms/all_motifs.txt
site-packages/snakehichiptf/organisms/basic.txt
site-packages/snakehichiptf/rules/Diffhichip.Snakefile
site-packages/snakehichiptf/rules/Genomesetup.Snakefile
site-packages/snakehichiptf/rules/Snakehichip.Snakefile
site-packages/snakehichiptf/rules/TFscprinter.Snakefile
site-packages/snakehichiptf/rules/TFtobias.Snakefile
site-packages/snakehichiptf/rules/envs/basic.yaml
site-packages/snakehichiptf/rules/envs/cooler.yaml
site-packages/snakehichiptf/rules/envs/deeptools.yaml
site-packages/snakehichiptf/rules/envs/diffloop.yaml
site-packages/snakehichiptf/rules/envs/fithichip.yaml
site-packages/snakehichiptf/rules/envs/genomefeature.yaml
site-packages/snakehichiptf/rules/envs/hicdc.yaml
site-packages/snakehichiptf/rules/envs/hicexplorer.yaml
site-packages/snakehichiptf/rules/envs/hichipper.yaml
site-packages/snakehichiptf/rules/envs/hicpro.yaml
site-packages/snakehichiptf/rules/envs/maps.yaml
site-packages/snakehichiptf/rules/envs/mapsrun.yaml
site-packages/snakehichiptf/rules/envs/r.yaml
site-packages/snakehichiptf/rules/envs/samtools.yaml
site-packages/snakehichiptf/rules/envs/scprinter_gpu.yaml
site-packages/snakehichiptf/rules/envs/tobias.yaml
site-packages/snakehichiptf/scripts/MAPS.py
site-packages/snakehichiptf/scripts/MAPS_peak_formatting.r
site-packages/snakehichiptf/scripts/MAPS_regression_and_peak_caller.r
site-packages/snakehichiptf/scripts/chr2_scprinter_main.py
site-packages/snakehichiptf/scripts/feather_filter_all.py
site-packages/snakehichiptf/scripts/feather_filter_chr.py
site-packages/snakehichiptf/scripts/feather_filter_chr_hicpro.py
site-packages/snakehichiptf/scripts/feather_split_all.py
site-packages/snakehichiptf/scripts/feather_split_rongxin.py
site-packages/snakehichiptf/scripts/feature_frag2bin.py
site-packages/snakehichiptf/scripts/fithichip/BiasCalc.r
site-packages/snakehichiptf/scripts/fithichip/CombineNearbyInteraction.py
site-packages/snakehichiptf/scripts/fithichip/CombineREFragMappGC.r
site-packages/snakehichiptf/scripts/fithichip/ContactCountDistr.r
site-packages/snakehichiptf/scripts/fithichip/ContactMatDiffRes.sh
site-packages/snakehichiptf/scripts/fithichip/CoverageBin.py
site-packages/snakehichiptf/scripts/fithichip/CoverageBin.r
site-packages/snakehichiptf/scripts/fithichip/CreateBinMatrixFromBed.r
site-packages/snakehichiptf/scripts/fithichip/DiffAnalysisHiChIP.r
site-packages/snakehichiptf/scripts/fithichip/Distance_vs_CC.r
site-packages/snakehichiptf/scripts/fithichip/Extract_contactMat_HiC.py
site-packages/snakehichiptf/scripts/fithichip/Filt_Loop_DistThr.r
site-packages/snakehichiptf/scripts/fithichip/FitHiC_SigInt.r
site-packages/snakehichiptf/scripts/fithichip/HiC_Simulate_by_ChIP_Coverage.r
site-packages/snakehichiptf/scripts/fithichip/Interaction.r
site-packages/snakehichiptf/scripts/fithichip/InteractionHicPro.r
site-packages/snakehichiptf/scripts/fithichip/InteractionPlots.r
site-packages/snakehichiptf/scripts/fithichip/Interaction_Sort_Genomic_Distance.r
site-packages/snakehichiptf/scripts/fithichip/MergeBAMInferPeak.sh
site-packages/snakehichiptf/scripts/fithichip/PackageTest.r
site-packages/snakehichiptf/scripts/fithichip/PeakInferHiChIP.sh
site-packages/snakehichiptf/scripts/fithichip/PlotGenomeBins.r
site-packages/snakehichiptf/scripts/fithichip/Process_contactMat_HiC.py
site-packages/snakehichiptf/scripts/fithichip/Significance_Features.r
site-packages/snakehichiptf/scripts/fithichip/SummaryFitHiChIP.sh
site-packages/snakehichiptf/scripts/fithichip/result_summary.r
site-packages/snakehichiptf/scripts/fithichip/scripts/hichip_peak_call_script.sh
site-packages/snakehichiptf/scripts/fithichip/scripts/sample_script.sh
site-packages/snakehichiptf/scripts/generate_site_positions_yq.py
site-packages/snakehichiptf/scripts/hicdc_differential_interactions.R
site-packages/snakehichiptf/scripts/hicdc_genomefeature.R
site-packages/snakehichiptf/scripts/hicdc_significant_interactions.R
site-packages/snakehichiptf/scripts/hichipper.diffloop_differential_analysis.R
site-packages/snakehichiptf/scripts/hichipper.diffloop_work.R
site-packages/snakehichiptf/scripts/hicpro-3.1.0/Makefile
site-packages/snakehichiptf/scripts/hicpro-3.1.0/bin/HiC-Pro
site-packages/snakehichiptf/scripts/hicpro-3.1.0/bin/utils/digest_genome.py
site-packages/snakehichiptf/scripts/hicpro-3.1.0/bin/utils/extract_snps.py
site-packages/snakehichiptf/scripts/hicpro-3.1.0/bin/utils/hicpro2fithic.py
site-packages/snakehichiptf/scripts/hicpro-3.1.0/bin/utils/hicpro2higlass.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/bin/utils/hicpro2juicebox.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/bin/utils/make_viewpoints.py
site-packages/snakehichiptf/scripts/hicpro-3.1.0/bin/utils/sparseToDense.py
site-packages/snakehichiptf/scripts/hicpro-3.1.0/bin/utils/split_reads.py
site-packages/snakehichiptf/scripts/hicpro-3.1.0/bin/utils/split_sparse.py
site-packages/snakehichiptf/scripts/hicpro-3.1.0/config-system.txt
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/Makefile
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/bowtie_combine.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/bowtie_pairing.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/bowtie_wrap.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/build_matrix
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/build_raw_maps.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/cutsite_trimming
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/hic.inc.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/ice
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/ice_norm.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/make_lsf_script.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/make_plots.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/make_sge_script.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/make_slurm_script.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/make_torque_script.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/mapped_2hic_dnase.py
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/mapped_2hic_fragments.py
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/mapped_2hic_fragments.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/mapping_stat.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/markAllelicStatus.py
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/mergeSAM.py
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/merge_statfiles.py
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/merge_stats.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/merge_valid_interactions.sh
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/onTarget.py
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/plot_hic_contacts.R
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/plot_hic_fragment.R
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/plot_mapping_portion.R
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/plot_pairing_portion.R
site-packages/snakehichiptf/scripts/hicpro-3.1.0/scripts/split_valid_interactions.py
site-packages/snakehichiptf/scripts/logger.py
site-packages/snakehichiptf/scripts/make_maps_runfile.py
site-packages/snakehichiptf/scripts/merge_map.py
site-packages/snakehichiptf/scripts/overlaps_gr1.tsv
site-packages/snakehichiptf/scripts/overlaps_gr2.tsv
site-packages/snakehichiptf/scripts/plot_footprints_scprinter_standalone.py
site-packages/snakehichiptf/scripts/qcReport_make.Rmd
site-packages/snakehichiptf/scripts/qc_all.R
site-packages/snakehichiptf/scripts/qc_hichip_barplot.R
site-packages/snakehichiptf/scripts/qc_hichip_quantiles.py
site-packages/snakehichiptf/scripts/qc_plot_quantiles.R
site-packages/snakehichiptf/scripts/restriction_cut_multipleenzyme.py
site-packages/snakehichiptf/scripts/scprinter_main.py
site-packages/snakehichiptf/scripts/singlecell_scprinter_main.py
site-packages/snakehichiptf/ui/__init__.py
site-packages/snakehichiptf/ui/launch.py
site-packages/snakehichiptf/ui/stl_app.py
site-packages/snakehichiptf/workflows/Diffhichip.py
site-packages/snakehichiptf/workflows/Genomesetup.py
site-packages/snakehichiptf/workflows/Snakehichip.py
site-packages/snakehichiptf/workflows/TFscprinter.py
site-packages/snakehichiptf/workflows/TFtobias.py
site-packages/snakehichiptf/workflows/__init__.py
