Files in tanaylab/gpatterns
Single Molecule Methylation Patterns Analysis Suite
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/RcppExports.R
R/TGL_kmeans.R
R/avg_meth.R
R/bissli2.R
R/chipseq.R
R/cluster.R
R/defs.R
R/demultiplex.R
R/epipoly.R
R/gpatterns-package.r
R/gpwm.R
R/gutils.R
R/import.R
R/map.R
R/merge-tidy_cpgs.R
R/patterns.R
R/pipeline.R
R/qc.R
R/utils.R
R/zzz.R
README.Rmd
README.md
exec/sgjob.sh
inst/bin/TGLKMeans_static
inst/bin/adjust_read_pos.R
inst/bin/conv_stats.py
inst/bin/mpms
inst/bin/sgjob.sh
inst/bissli2/bissli2-align.pl
inst/bissli2/bissli2-build.pl
inst/import/filter_dups_cpgs.py
inst/import/indexes.csv
inst/import/map_fastq.py
inst/import/reads.py
inst/import/split_fastq.py
inst/import/tidy_cpgs.py
man/TGL_kmeans.Rd
man/TGL_kmeans2.Rd
man/build_pallette.Rd
man/cume_dist_min.Rd
man/dot-gpatterns.bam2reads.Rd
man/dot-gpatterns.ds_stats.Rd
man/dot-gpatterns.filter_ontar_reads.Rd
man/dot-gpatterns.reads_per_umi.Rd
man/gbin_intervals.Rd
man/gcluster.run2.Rd
man/gextract.left_join.Rd
man/gintervals.filter.Rd
man/gintervals.neighbors1.Rd
man/glply.Rd
man/gpatterns.Rd
man/gpatterns.adjust_read_pos.Rd
man/gpatterns.apply_tidy_cpgs.Rd
man/gpatterns.bissli2.Rd
man/gpatterns.bissli2_build.Rd
man/gpatterns.border_pattern.Rd
man/gpatterns.calc_bipolarity.Rd
man/gpatterns.calc_epipoly.Rd
man/gpatterns.capture_stats.Rd
man/gpatterns.chip2peaks.Rd
man/gpatterns.clean_pattern.Rd
man/gpatterns.conv_stats.Rd
man/gpatterns.count_cpgs.Rd
man/gpatterns.create_patterns_track.Rd
man/gpatterns.downsample_patterns.Rd
man/gpatterns.epipoly_plot.Rd
man/gpatterns.extract.Rd
man/gpatterns.extract_all.Rd
man/gpatterns.extract_patterns.Rd
man/gpatterns.filter_by_dist.Rd
man/gpatterns.filter_cpgs.Rd
man/gpatterns.filter_loci.Rd
man/gpatterns.frag_stats.Rd
man/gpatterns.get_avg_meth.Rd
man/gpatterns.get_bg_meth.Rd
man/gpatterns.get_fragment_cov.Rd
man/gpatterns.get_pat_cov.Rd
man/gpatterns.get_pipeline_stats.Rd
man/gpatterns.get_promoters.Rd
man/gpatterns.get_tcpgs_stats.Rd
man/gpatterns.get_tidy_cpgs.Rd
man/gpatterns.global_meth_trend.Rd
man/gpatterns.import_from_bam.Rd
man/gpatterns.import_from_tidy_cpgs.Rd
man/gpatterns.impute.Rd
man/gpatterns.intervals_coverage.Rd
man/gpatterns.intervs_to_pat_space.Rd
man/gpatterns.ls.Rd
man/gpatterns.merge_tidy_cpgs.Rd
man/gpatterns.merge_tracks.Rd
man/gpatterns.pipeline.Rd
man/gpatterns.plot_cg_cor.Rd
man/gpatterns.plot_chip_quantiles.Rd
man/gpatterns.putative_enhancers.Rd
man/gpatterns.rm.Rd
man/gpatterns.screen_by_coverage.Rd
man/gpatterns.separate_strands.Rd
man/gpatterns.set_parallel.Rd
man/gpatterns.smoothScatter.Rd
man/gpatterns.spatial_meth_trend.Rd
man/gpatterns.tidy_cpgs_2_pat_freq.Rd
man/gpatterns.tidy_cpgs_2_pileup.Rd
man/gpatterns.tidy_cpgs_to_pats.Rd
man/gpatterns.track_exists.Rd
man/gpatterns.track_pat_space.Rd
man/gpatterns.track_stats.Rd
man/gpatterns.tracks_to_pat_space.Rd
man/gtrack.array.import_from_df.Rd
man/gtrack.import_mappedseq_bam.Rd
man/gvextract.Rd
man/mpms.Rd
man/p_smoothScatter.Rd
man/pheatmap1.Rd
src/Makevars
src/MethylPatternData.cpp
src/MethylPatternData.h
src/MethylPatternMixtureModel.cpp
src/MethylPatternMixtureModel.h
src/MethylPatternMixtureModelGainLoss.cpp
src/MethylPatternMixtureModelGainLoss.h
src/MethylPatternMixtureModelOneNoise.cpp
src/MethylPatternMixtureModelOneNoise.h
src/MethylPatternMixtureModelOneNoiseFixedMix.cpp
src/MethylPatternMixtureModelOneNoiseFixedMix.h
src/MethylPatternMixtureModelScanner.cpp
src/MethylPatternMixtureModelScanner.h
src/MethylPatternMixtureModelScannerGainLoss.cpp
src/MethylPatternMixtureModelScannerGainLoss.h
src/MethylPatternMixtureModelScannerOneNoise.cpp
src/MethylPatternMixtureModelScannerOneNoise.h
src/MethylPatternMixtureModelScannerOneNoiseFixedMix.cpp
src/MethylPatternMixtureModelScannerOneNoiseFixedMix.h
src/MethylPatternMixtureModelsCompare.cpp
src/MethylPatternMixtureModelsCompare.h
src/MethylPatternMixtureTester.cpp
src/MethylPatternMixtureTester.h
src/MethylPatternUniModel.cpp
src/MethylPatternUniModel.h
src/MethylPatternUniModelGainLoss.cpp
src/MethylPatternUniModelGainLoss.h
src/MethylPatternUniModelOneNoise.cpp
src/MethylPatternUniModelOneNoise.h
src/MixtureModel.cpp
src/MixtureModel.h
src/ModelData.cpp
src/ModelData.h
src/ModelDataMultiGroup.cpp
src/ModelDataMultiGroup.h
src/RcppExports.cpp
src/SamplingUtil.h
src/UniModel.cpp
src/UniModel.h
src/UniformModel.cpp
src/UniformModel.h
src/mpms.cpp
src/util.h
tests/testthat.R
vignettes/import.Rmd
