Files in chenweng1991/scMitoTracing
R package for Regulatory multi-omics with Deep Mitochondrial mutation profiling

.RData
.Rbuildignore
.Rhistory
.gitignore
.ipynb_checkpoints/Get_Started-checkpoint.ipynb
.ipynb_checkpoints/ReDeeM_R.RunningTest-checkpoint.ipynb
.ipynb_checkpoints/scMitoTracingRunningTest-checkpoint.ipynb
DESCRIPTION
Extra.R
Get_Started.ipynb
LICENSE
NAMESPACE
PythonHelper/ComputeLikli.py
R/BuidTree.R R/Clustering_functions.R R/General_functions.R R/Plot.R R/VariantSummary.R
R/log
README.md
ReDeeM_R.RunningTest.ipynb
activate.R data-raw/DATASET.R
data/ATACWhite.rda
data/CellPCT.rda
data/ContextsDic.rda
data/Griffin_Signatures.rda
data/RNAWhite.rda
data/all.genes.refer.rda
data/msig.db.rda
data/ref_all_long.rda
docs/404.html
docs/LICENSE-text.html
docs/articles/index.html
docs/articles/package_intro.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/ATAC_Wrapper.html
docs/reference/AddDatatoplot_clustering-mitoTracing-method.html
docs/reference/AddDatatoplot_clustering-redeemR-method.html
docs/reference/AddDatatoplot_clustering.html
docs/reference/AddDist-mitoTracing-method.html
docs/reference/AddDist-redeemR-method.html
docs/reference/AddDist.html
docs/reference/AddHemSignature.html
docs/reference/AddTree-mitoTracing-method.html
docs/reference/AddTree-redeemR-method.html
docs/reference/AddTree.html
docs/reference/Add_AssignVariant-mitoTracing-method.html
docs/reference/Add_AssignVariant-redeemR-method.html
docs/reference/Add_AssignVariant.html
docs/reference/Add_DepthMatrix-mitoTracing-method.html
docs/reference/Add_DepthMatrix-redeemR-method.html
docs/reference/Add_DepthMatrix.html
docs/reference/Add_tree_cut-mitoTracing-method.html
docs/reference/Add_tree_cut-redeemR-method.html
docs/reference/Add_tree_cut.html
docs/reference/BinaryDist.html
docs/reference/CV.html
docs/reference/CW_mgatk.read.html
docs/reference/Clone_FinderMarker.html
docs/reference/ComputeRejectRate.html
docs/reference/CountVperCell.html
docs/reference/Create_mitoTracing.html
docs/reference/Create_redeemR.html
docs/reference/DE.gettripple.html
docs/reference/Datatoplots-class.html
docs/reference/DepthSummary.html
docs/reference/DistObjects-class.html
docs/reference/DoDE.html
docs/reference/FromDist2Graph.html
docs/reference/GEM_Wrapper.html
docs/reference/GTSummary.html
docs/reference/Get_Clonal_Variants.html
docs/reference/LineageBiasPlot.html
docs/reference/MakeAllNodes.html
docs/reference/MakeDF4Regress.html
docs/reference/MakeNN.html
docs/reference/Make_AnnTable.html
docs/reference/Make_Cells4Nodes.html
docs/reference/Make_matrix-mitoTracing-method.html
docs/reference/Make_matrix-redeemR-method.html
docs/reference/Make_matrix.html
docs/reference/Make_tree-mitoTracing-method.html
docs/reference/Make_tree-redeemR-method.html
docs/reference/Make_tree.html
docs/reference/MergeMtx.html
docs/reference/Motifenrich.binom.html
docs/reference/Multi_Wrapper.html
docs/reference/MutationProfile.bulk.html
docs/reference/NN2M.html
docs/reference/ProgenyMapping.html
docs/reference/ProgenyMapping_np.html
docs/reference/Reclustering.html
docs/reference/Reclustering_hm.html
docs/reference/Rplot001.png
docs/reference/Run_Lin_regression.html
docs/reference/Run_Lin_regression_poi.html
docs/reference/Runplot_scale_2.html
docs/reference/Runplot_scale_3.html
docs/reference/SeuratLSIClustering-mitoTracing-method.html
docs/reference/SeuratLSIClustering-redeemR-method.html
docs/reference/SeuratLSIClustering.html
docs/reference/Show_Consensus.html
docs/reference/Subset_MitoTracing.html
docs/reference/Subset_redeemR.html
docs/reference/TREE-class.html
docs/reference/Tomerge_v2.html
docs/reference/Translate_RNA2ATAC.html
docs/reference/Translate_simple_ATAC2RNA.html
docs/reference/Translate_simple_RNA2ATAC.html
docs/reference/Vfilter_v3.html
docs/reference/Vfilter_v4.html
docs/reference/add_derived_profile_info.html
docs/reference/df2ProfileMtx.html
docs/reference/get_ancestral_nodes.html
docs/reference/index.html
docs/reference/mitoTracing-class.html
docs/reference/plot_depth.html
docs/reference/plot_npSummary.html
docs/reference/plot_variant.html
docs/reference/quick_w_cosine.html
docs/reference/quick_w_jaccard.html
docs/reference/reconstruct_genotype_summary.html
docs/reference/redeemR-class.html
docs/reference/redeemR.read.html
docs/reference/show-mitoTracing-method.html
docs/reference/show-redeemR-method.html
docs/reference/split_profile.html
docs/reference/str2vector.html
docs/sitemap.xml
log
man/ATAC_Wrapper.Rd man/AddDatatoplot_clustering-redeemR-method.Rd man/AddDatatoplot_clustering.Rd man/AddDist-redeemR-method.Rd man/AddDist.Rd man/AddDist_legacy-mitoTracing-method.Rd man/AddDist_legacy.Rd man/AddHemSignature.Rd man/AddTree-redeemR-method.Rd man/AddTree.Rd man/Add_AssignVariant-redeemR-method.Rd man/Add_AssignVariant.Rd man/Add_DepthMatrix-redeemR-method.Rd man/Add_DepthMatrix.Rd man/Add_tree_cut-redeemR-method.Rd man/Add_tree_cut.Rd man/AddsigTag.6.new.Rd man/BinaryDist.Rd man/CV.Rd man/CW_mgatk.read.Rd man/Clone_FinderMarker.Rd man/ComputeRejectRate.Rd man/ComputeRejectRate_legacy.Rd man/CountVperCell.Rd man/Create_mitoTracing.Rd man/Create_redeemR.Rd man/DE.gettripple.Rd man/Datatoplots-class.Rd man/DepthSummary.Rd man/DistObjects-class.Rd man/DoDE.Rd man/FromDist2Graph.Rd man/Fun.enrich_withFC.Rd man/Fun.enrich_withFC.pvalue.Rd man/GEM_Wrapper.Rd man/GTSummary.Rd man/Get_Clonal_Variants.Rd man/Getgenenumber.Rd man/Getpallet2.Rd man/LineageBiasPlot.Rd man/MakeAllNodes.Rd man/MakeDF4Regress.Rd man/MakeNN.Rd man/Make_AnnTable.Rd man/Make_Cells4Nodes.Rd man/Make_matrix-redeemR-method.Rd man/Make_matrix.Rd man/Make_tree-redeemR-method.Rd man/Make_tree.Rd man/Make_tree_legacy-mitoTracing-method.Rd man/Make_tree_legacy.Rd man/MergeMtx.Rd man/Motifenrich.binom.Rd man/Multi_Wrapper.Rd man/MutationProfile.bulk.Rd man/NN2M.Rd man/ProgenyMapping.Rd man/ProgenyMapping_np.Rd man/Reclustering.Rd man/Reclustering_hm.Rd man/Run_Lin_regression.Rd man/Run_Lin_regression_poi.Rd man/Runplot_scale_2.Rd man/Runplot_scale_3.Rd man/SeuratLSIClustering-redeemR-method.Rd man/SeuratLSIClustering.Rd man/Show_Consensus.Rd man/Subset_redeemR.Rd man/TREE-class.Rd man/Tomerge.col.Rd man/Tomerge_v2.Rd man/Translate_RNA2ATAC.Rd man/Translate_simple_ATAC2RNA.Rd man/Translate_simple_RNA2ATAC.Rd man/Vfilter_v3.Rd man/Vfilter_v4.Rd man/add_derived_profile_info.Rd man/binomialtest.msig.enrch_deplet.Rd man/convert_mitotracing_redeemR.Rd man/df2ProfileMtx.Rd man/get_ancestral_nodes.Rd man/gsea_enrichmentheat.Rd man/mitoTracing-class.Rd man/plot_depth.Rd man/plot_depth_legacy.Rd man/plot_npSummary.Rd man/plot_variant.Rd man/plot_variant_legacy.Rd man/quick_w_cosine.Rd man/quick_w_jaccard.Rd man/reconstruct_genotype_summary.Rd man/redeemR-class.Rd man/redeemR.read.Rd man/show-redeemR-method.Rd man/split_profile.Rd man/str2vector.Rd redeemR_1.0.pdf
renv.lock
trash/NAMESPACE
trash/NEWS.md trash/REDEEM-R_0.0.0.9000.pdf
vignettes/.gitignore
vignettes/vignettes.md
chenweng1991/scMitoTracing documentation built on July 2, 2024, 8:41 p.m.