├── .gitignore ├── .travis.yml ├── CONTRIBUTORS ├── LICENSE ├── MANIFEST.in ├── README.md ├── Snakefile ├── config_example.yaml ├── examples ├── DNase_cluster_ACTB.bed.gz ├── GRCh38-ACTB-locus.gtf.gz ├── NA19240-methylation_ACTB_calls.tsv.gz ├── NA19240-methylation_ACTB_frequency.tsv.gz └── test.sh ├── extra_scripts ├── assoc_hap_meth.py ├── merge_simplified_meths.py ├── paircor.py ├── per_read_methylation.py ├── plot_hap_meth.py ├── plot_methylation_per_allele.py ├── plot_methylation_per_allele_2.py └── simplify_haplotype_specific_meth.py ├── methplotlib ├── __init__.py ├── annotation.py ├── differential │ ├── __init__.py │ └── differential.py ├── examples │ ├── ACTB_calls.tsv.gz │ ├── DNAse_cluster.bed.gz │ ├── g38_locus.gtf.gz │ ├── meth_freq.tsv.gz │ └── test.sh ├── helpers.py ├── import_methylation.py ├── methplotlib.py ├── plots.py ├── qc.py ├── utils.py └── version.py ├── scripts ├── __init__.py ├── allele_specific_modification ├── annotate_calls_by_phase.py ├── calculate_methylation_frequency.py ├── differential_modification ├── genome-wide-QC.py ├── sorting_and_multiple_testing_correction.py ├── split_calls_by_longshot_phase.py └── split_calls_by_phase.py ├── setup.py └── tests ├── chr21.bed.gz ├── d1.tsv.gz ├── d2.tsv.gz ├── result.txt ├── result_diff.tsv.gz └── test_differential.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/.travis.yml -------------------------------------------------------------------------------- /CONTRIBUTORS: -------------------------------------------------------------------------------- 1 | Endre Bakken Stovner -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include README.md 2 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/README.md -------------------------------------------------------------------------------- /Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/Snakefile -------------------------------------------------------------------------------- /config_example.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/config_example.yaml -------------------------------------------------------------------------------- /examples/DNase_cluster_ACTB.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/examples/DNase_cluster_ACTB.bed.gz -------------------------------------------------------------------------------- /examples/GRCh38-ACTB-locus.gtf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/examples/GRCh38-ACTB-locus.gtf.gz -------------------------------------------------------------------------------- /examples/NA19240-methylation_ACTB_calls.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/examples/NA19240-methylation_ACTB_calls.tsv.gz -------------------------------------------------------------------------------- /examples/NA19240-methylation_ACTB_frequency.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/examples/NA19240-methylation_ACTB_frequency.tsv.gz -------------------------------------------------------------------------------- /examples/test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/examples/test.sh -------------------------------------------------------------------------------- /extra_scripts/assoc_hap_meth.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/extra_scripts/assoc_hap_meth.py -------------------------------------------------------------------------------- /extra_scripts/merge_simplified_meths.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/extra_scripts/merge_simplified_meths.py -------------------------------------------------------------------------------- /extra_scripts/paircor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/extra_scripts/paircor.py -------------------------------------------------------------------------------- /extra_scripts/per_read_methylation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/extra_scripts/per_read_methylation.py -------------------------------------------------------------------------------- /extra_scripts/plot_hap_meth.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/extra_scripts/plot_hap_meth.py -------------------------------------------------------------------------------- /extra_scripts/plot_methylation_per_allele.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/extra_scripts/plot_methylation_per_allele.py -------------------------------------------------------------------------------- /extra_scripts/plot_methylation_per_allele_2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/extra_scripts/plot_methylation_per_allele_2.py -------------------------------------------------------------------------------- /extra_scripts/simplify_haplotype_specific_meth.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/extra_scripts/simplify_haplotype_specific_meth.py -------------------------------------------------------------------------------- /methplotlib/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /methplotlib/annotation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/methplotlib/annotation.py -------------------------------------------------------------------------------- /methplotlib/differential/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /methplotlib/differential/differential.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/methplotlib/differential/differential.py -------------------------------------------------------------------------------- /methplotlib/examples/ACTB_calls.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/methplotlib/examples/ACTB_calls.tsv.gz -------------------------------------------------------------------------------- /methplotlib/examples/DNAse_cluster.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/methplotlib/examples/DNAse_cluster.bed.gz -------------------------------------------------------------------------------- /methplotlib/examples/g38_locus.gtf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/methplotlib/examples/g38_locus.gtf.gz -------------------------------------------------------------------------------- /methplotlib/examples/meth_freq.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/methplotlib/examples/meth_freq.tsv.gz -------------------------------------------------------------------------------- /methplotlib/examples/test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/methplotlib/examples/test.sh -------------------------------------------------------------------------------- /methplotlib/helpers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/methplotlib/helpers.py -------------------------------------------------------------------------------- /methplotlib/import_methylation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/methplotlib/import_methylation.py -------------------------------------------------------------------------------- /methplotlib/methplotlib.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/methplotlib/methplotlib.py -------------------------------------------------------------------------------- /methplotlib/plots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/methplotlib/plots.py -------------------------------------------------------------------------------- /methplotlib/qc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/methplotlib/qc.py -------------------------------------------------------------------------------- /methplotlib/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/methplotlib/utils.py -------------------------------------------------------------------------------- /methplotlib/version.py: -------------------------------------------------------------------------------- 1 | __version__ = "0.22.0" 2 | -------------------------------------------------------------------------------- /scripts/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scripts/allele_specific_modification: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/scripts/allele_specific_modification -------------------------------------------------------------------------------- /scripts/annotate_calls_by_phase.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/scripts/annotate_calls_by_phase.py -------------------------------------------------------------------------------- /scripts/calculate_methylation_frequency.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/scripts/calculate_methylation_frequency.py -------------------------------------------------------------------------------- /scripts/differential_modification: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/scripts/differential_modification -------------------------------------------------------------------------------- /scripts/genome-wide-QC.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/scripts/genome-wide-QC.py -------------------------------------------------------------------------------- /scripts/sorting_and_multiple_testing_correction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/scripts/sorting_and_multiple_testing_correction.py -------------------------------------------------------------------------------- /scripts/split_calls_by_longshot_phase.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/scripts/split_calls_by_longshot_phase.py -------------------------------------------------------------------------------- /scripts/split_calls_by_phase.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/scripts/split_calls_by_phase.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/setup.py -------------------------------------------------------------------------------- /tests/chr21.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/tests/chr21.bed.gz -------------------------------------------------------------------------------- /tests/d1.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/tests/d1.tsv.gz -------------------------------------------------------------------------------- /tests/d2.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/tests/d2.tsv.gz -------------------------------------------------------------------------------- /tests/result.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/tests/result.txt -------------------------------------------------------------------------------- /tests/result_diff.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/tests/result_diff.tsv.gz -------------------------------------------------------------------------------- /tests/test_differential.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wdecoster/methplotlib/HEAD/tests/test_differential.py --------------------------------------------------------------------------------