Files in jakeyeung/scChIX
Deconvolving Multiplexed Histone Modifications in Single Cells.

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DESCRIPTION

NAMESPACE

analysis_scripts/H3K9me3-H3K36me3_gastrulation_analysis/test.R

analysis_scripts/unfixed/2-scchix_downstream_analysis.R

analysis_scripts/unfixed/check_intermediates.r analysis_scripts/unfixed/unfixed_10kb_LDA_downstream.R analysis_scripts/unfixed/unfixed_10kb_prepare_mats.R analysis_scripts/unfixed/unfixed_10kb_prepare_mats.TSS.R analysis_scripts/unfixed/unfixed_10kb_prepare_mats.common_rows_genomewide.R

data/CountMatsGastrulationInputs.RData.REMOVED.git-id

data/GastrulationLouvainCelltypeAnnotations.RData

data/GastrulationScChIXOutputsK36K9m3.RData

data/GroundTruthLabels.RData

data/H3K27me3_LdaOutputs.RData

data/H3K27me3_ProjectionOutput.RData

data/H3K9me3_LdaOutputs.RData

data/H3K9me3_ProjectionOutput.RData

data/MacDiffDblMatForSplitting_H3K4me1xH3K36me3.RData

data/MacDiffDblMatNearestNeighbors.RData

data/MacDiffDblMat_H3K4me1xH3K36me3.RData

data/MacDiffMetadata_H3K4me1xH3K36me3.RData

data/MacDiffProjectionOutput_H3K36me3.RData

data/MacDiffProjectionOutput_H3K4me1.RData

data/ModelFromSingleForFitting.RData

data/OrganoMetadata.RData

data/OrganoProjOutput_H3K36me3.RData

data/OrganoProjOutput_H3K9me3.RData

data/RawDblCountMatSubset.RData

data/Simulation_scChIX_Outputs.RData

data/scChIXOutputs_H3K4me1xH3K36me3.RData

example_umap.png

inst/extdata/cellbarcodes_384_NLA_annotated.bc

inst/extdata/countmat_var_filt.mark1-mark2.rds

inst/extdata/countmat_var_filt.mark1.rds

inst/extdata/countmat_var_filt.mark2.rds

interactive_scripts/1-save_LDA_objs_for_projections.R interactive_scripts/1-save_projection_objs_all_cells.R interactive_scripts/1-subset_cells_for_fitting.R interactive_scripts/1-subset_cells_for_fitting_LoadFromInteractiveScripts.R interactive_scripts/1-subset_cells_for_fitting_ThreeClusters.R interactive_scripts/2-fit_model_on_subset.R man/ClipLast.Rd man/ConcatMat.Rd man/FitAsympMarks.UpOrDown.Rd man/FitMixingWeight.Rd man/FitMixingWeightPtimeLinear.fixedw.Rd man/GetDayFromCellByRow.Rd man/GetDayFromCellDataFrame.Rd man/GetLLMerged.Rd man/IsUpOrDown.Rd man/MeanAcrossClusters.Rd man/SetupDatForGene.UpOrDown.Rd man/SimulateChICseq.Rd man/SoftMax.Rd man/UnmixRawCounts.Rd

processing_scripts/demultiplexing_pipeline/pipeline_directly_from_LDA/0-run.celltyping_from_LDA_gastru.Genomewide.sh

processing_scripts/demultiplexing_pipeline/pipeline_directly_from_LDA/0-run.celltyping_from_LDA_gastru.TopBinsFilt.sh

processing_scripts/demultiplexing_pipeline/pipeline_directly_from_LDA/0-run.setup_lda_countmat_metas.TopBinsFilt.sh

processing_scripts/demultiplexing_pipeline/pipeline_directly_from_LDA/0-run.setup_lda_countmat_metas.sh

processing_scripts/demultiplexing_pipeline/pipeline_directly_from_LDA/1-run.setup_objs_for_unmixing.varfilt.TopBinsFilt.sh

processing_scripts/demultiplexing_pipeline/pipeline_directly_from_LDA/1-run.setup_objs_for_unmixing.varfilt.genomewide.sh

processing_scripts/demultiplexing_pipeline/pipeline_directly_from_LDA/2-run.load_objs_run_fits.TopBinsFilt.sh

processing_scripts/demultiplexing_pipeline/pipeline_directly_from_LDA/2-run.load_objs_run_fits.genomewide.sh

processing_scripts/demultiplexing_pipeline/pipeline_directly_from_LDA/3-run_unmixing_downstream_split.Genomewide.marks.sh

processing_scripts/demultiplexing_pipeline/pipeline_directly_from_LDA/3-run_unmixing_downstream_split.TopBinsFilt.marks.sh

processing_scripts/demultiplexing_pipeline/pipeline_directly_from_LDA/4-project_LDA_after_unmixing.GenomeWide.marks.sh

processing_scripts/demultiplexing_pipeline/pipeline_directly_from_LDA/4-project_LDA_after_unmixing.TopBinsFilt.marks.sh

processing_scripts/preprocessing/0-copy_counts_from_MF.sh

processing_scripts/preprocessing/1-copy_demux_fastqs_dbl.sh

processing_scripts/preprocessing/1-copy_demux_fastqs_single.again_K27me3_only.sh

processing_scripts/preprocessing/1-copy_demux_fastqs_single.sh

processing_scripts/preprocessing/2-trim_fastqs.K27me3_singles.sh

processing_scripts/preprocessing/2-trim_fastqs.sh

processing_scripts/preprocessing/3-map_fastqs.sh

processing_scripts/preprocessing/3-map_fastqs_multicore.sh

processing_scripts/preprocessing/3-map_fastqs_multicore_H3K27me3_singles.sh

processing_scripts/preprocessing/3-remap_E10p5_K9m3_fastqs.sh

processing_scripts/preprocessing/4-sort_index_bam.sh

processing_scripts/preprocessing/4-sort_index_tag_bam.H3K27me3_E8.sh

processing_scripts/preprocessing/4-sort_index_tag_bam.sh

processing_scripts/preprocessing/4-tag_bam.sh

processing_scripts/preprocessing/5-make_count_tables.RZ_counts.NewFilters.K27me3only.sh

processing_scripts/preprocessing/5-make_count_tables.RZ_counts.NewFilters.sh

processing_scripts/preprocessing/5-make_count_tables_K36_genebodies_K9m3_bins.sh

processing_scripts/preprocessing/5-make_count_tables_TES.K27me3only.sh

processing_scripts/preprocessing/5-make_count_tables_TES.sh

processing_scripts/preprocessing/5-make_count_tables_TSS.sh

processing_scripts/preprocessing/5-make_count_tables_from_tagged_bams.K27me3only.sh

processing_scripts/preprocessing/5-make_count_tables_from_tagged_bams.sh

processing_scripts/preprocessing/6-run.cbind_count_mats.K27me3only.sh

processing_scripts/preprocessing/6-run.cbind_count_mats.sh

processing_scripts/preprocessing/6-run.cbind_count_mats_TSS.sh

processing_scripts/preprocessing/6-run.cbind_count_mats_count_table_topfeatures_K36_genebodies_K9m3_bins.sh

processing_scripts/preprocessing/6-run.rbind_RZ_files.sh

processing_scripts/preprocessing/6-run_filter_cells.K27me3only.sh

processing_scripts/preprocessing/6-run_filter_cells.sh

processing_scripts/preprocessing/7-move_outputs.sh

processing_scripts/preprocessing/7-move_outputs_count_mats.sh

processing_scripts/preprocessing/7-move_outputs_count_mats_K36_genebodies_K9m3_bins.sh

processing_scripts/preprocessing/8-run_LDA_after_filtering.sh

processing_scripts/preprocessing/8-run_LDA_after_filtering_less_stringent.10kb.sh

processing_scripts/preprocessing/8-run_LDA_after_filtering_less_stringent.TES.sh

processing_scripts/preprocessing/8-run_LDA_after_filtering_less_stringent.TSS.sh

processing_scripts/preprocessing/8-run_LDA_after_filtering_less_stringent.sh

processing_scripts/preprocessing/8-run_LDA_after_filtering_less_stringent_cleanedup.sh

processing_scripts/preprocessing/8-run_LDA_after_filtering_less_stringent_cleanedup_TES.sh

processing_scripts/preprocessing/8-run_LDA_after_filtering_less_stringent_cleanedup_featurefilt.sh

processing_scripts/preprocessing/8-run_LDA_after_filtering_less_stringent_cleanedup_featurefilt_cellsfilt_Genebodies_Bins_merged.sh

processing_scripts/preprocessing/8-run_LDA_after_filtering_less_stringent_noLSIfilt.TopBins.sh

processing_scripts/preprocessing/8-run_LDA_after_filtering_less_stringent_noLSIfilt.sh

processing_scripts/preprocessing/8-run_LDA_after_filtering_varfilt.TopBins.sh

processing_scripts/preprocessing/8-run_LDA_after_filtering_varfilt.sh

processing_scripts/preprocessing_differentiation/1-run_demux.sh

processing_scripts/preprocessing_differentiation/2-trim_fastq.sh

processing_scripts/preprocessing_differentiation/3-map_fastqs.sh

processing_scripts/preprocessing_differentiation/4-sort_index_tag_bam.sh

processing_scripts/preprocessing_differentiation/5-make_count_tables.RZ_counts.NewFilters.sh

processing_scripts/preprocessing_differentiation/5-make_count_tables_from_tagged_bams.sh

processing_scripts/preprocessing_differentiation/5-make_count_tables_from_tagged_bams_from_TSS.sh

snakemake_workflow/Snakefile

snakemake_workflow/cluster.json

snakemake_workflow/config.yaml

snakemake_workflow/init_output_dirs.sh

snakemake_workflow/run_snakemake.gastru_K9.sh

snakemake_workflow/run_snakemake.simulation_data.sh

snakemake_workflow/run_snakemake_unfixed_10kb.sh

snakemake_workflow/scripts/0-run_LDA_initial.snakemake.sh

snakemake_workflow/scripts/1-run.setup_lda_countmat_metas.snakemake.sh

snakemake_workflow/scripts/2-run.setup_objs_for_unmixing.snakemake.sh

snakemake_workflow/scripts/3-run.load_objs_run_fits.snakemake.sh

snakemake_workflow/scripts/4-run_unmixing_downstream_split.snakemake.sh

snakemake_workflow/scripts/5-project_LDA_after_unmixing.snakemake.sh

snakemake_workflow/scripts/5-run_LDA_after_unmixing.snakemmake.sh

utils/cbind_count_mats.R utils/cluster_make_lda_countmat_metadata_objects.R utils/filter_cells_by_totalcuts_TAfrac_intrachromovar.R utils/infer_celltype_from_LDA_late_gastrulation.R utils/load_objs_run_fits.R

utils/make_cuts_in_regions.py

utils/project_new_samples_on_LDA_bin.R utils/rbind_RZ_files.R

utils/remove_duplicated_rows_bams.py

utils/run_LDA_model2.R utils/run_LDA_model3.R utils/setup_objs_for_unmixing_general_from_LDA_or_countmat.R utils/setup_objs_for_unmixing_topics_general.R

utils/split_double_BAM.py

utils/split_double_BAM_with_interpolation.py

utils/unmixing_downstream_split_reads_script.UnevenRows.R

vignettes/.gitignore

vignettes/scChIX-bonemarrow-k4me1k27me3-vignette.Rmd vignettes/scChIX-gastrulation.Rmd vignettes/scChIX-gastrulation.md

vignettes/scChIX-gastrulation_files/figure-markdown_github/ratios-1.png

vignettes/scChIX-gastrulation_files/figure-markdown_github/wrangle-scchix-1.png

vignettes/scChIX-macrophagedifferentiation-fit_exponentials_to_pseudotime.Rmd vignettes/scChIX-macrophagedifferentiation-fit_exponentials_to_pseudotime_downstream_velocities.Rmd vignettes/scChIX-macrophagedifferentiation-split_dblcounts_project_to_UMAP.Rmd vignettes/scChIX-macrophagedifferentiation.Rmd vignettes/scChIX-macrophagedifferentiation.md

vignettes/scChIX-macrophagedifferentiation_files/figure-markdown_github/dblptimeplot-1.png

vignettes/scChIX-simulation.Rmd vignettes/scChIX-simulation.md

vignettes/scChIX-simulation_files/figure-markdown_github/check-1.png

vignettes/scChIX-simulation_files/figure-markdown_github/check-2.png

vignettes/scChIX-simulation_files/figure-markdown_github/check-3.png

vignettes/scChIX-simulation_files/figure-markdown_github/ci-1.png

vignettes/scChIX-simulation_files/figure-markdown_github/ci-2.png

vignettes/scChIX-simulation_files/figure-markdown_github/ci-3.png

vignettes/scChIX-simulation_files/figure-markdown_github/ci-4.png

vignettes/scChIX-simulation_files/figure-markdown_github/generate_counts-1.png

vignettes/scChIX-simulation_files/figure-markdown_github/generate_counts-2.png

vignettes/scChIX-simulation_files/figure-markdown_github/generate_counts-3.png

vignettes/scChIX-simulation_files/figure-markdown_github/hist-1.png

vignettes/scChIX-simulation_files/figure-markdown_github/hist-2.png

vignettes/scChIX-simulation_files/figure-markdown_github/hist-3.png

vignettes/scChIX-simulation_files/figure-markdown_github/hist-4.png

vignettes/scChIX-simulation_files/figure-markdown_github/hist-5.png

vignettes/scChIX-simulation_files/figure-markdown_github/hist-6.png

vignettes/scChIX-simulation_files/figure-markdown_github/hist-7.png

vignettes/scChIX-simulation_files/figure-markdown_github/hist-8.png

vignettes/scChIX-simulation_files/figure-markdown_github/umap-1.png

vignettes/scChIX-vignette.Rmd vignettes/scChIX-vignette.md

vignettes/scChIX-vignette_files/figure-markdown_github/plot_umap2-1.png

vignettes/scChIX-vignette_files/figure-markdown_github/visualize_all_cells-1.png

vignettes/scChIX-vignette_files/figure-markdown_github/visualize_one_cell-1.png

jakeyeung/scChIX documentation built on May 7, 2023, 9:14 a.m.

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jakeyeung/scChIX
Deconvolving Multiplexed Histone Modifications in Single Cells.

Files in jakeyeung/scChIX
Deconvolving Multiplexed Histone Modifications in Single Cells.

R Package Documentation

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jakeyeung/scChIX Deconvolving Multiplexed Histone Modifications in Single Cells.

Files in jakeyeung/scChIX Deconvolving Multiplexed Histone Modifications in Single Cells.

R Package Documentation

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We want your feedback!

jakeyeung/scChIX
Deconvolving Multiplexed Histone Modifications in Single Cells.

Files in jakeyeung/scChIX
Deconvolving Multiplexed Histone Modifications in Single Cells.