Files in Yutong441/TBdev
Infer a Trophoblast Developmental Trajectory

.Rbuildignore

.gitattributes

.gitignore

DESCRIPTION

NAMESPACE

R/Ax2D.R R/Ax3D.R R/DE_gene.R R/GPLVM_utils.R R/Lab3D.R R/SCHeat.R R/SCHeat_split.R R/TF_motif.R R/WGCNA_utils.R R/arrange_figures.R R/arrange_poster.R R/batch_correct.R R/clean_terms.R R/compare_DE.R R/cycle_analysis.R R/data.R R/dim_red.R R/divergence.R R/enrich_multi.R R/enrichment.R R/expr_mat.R R/format.R R/general.R R/graph_abstract.R R/img_preprocess.R R/line_break.R R/marker_list.R R/overRep.R R/pathway.R R/plot_DR_2D.R R/plot_DR_3D.R R/plot_network.R R/quad_prog.R R/sim_emapplot.R R/similarity.R R/switch_point.R README.md data-raw/DATASET.R data-raw/TF.R data-raw/cell_markers.R data-raw/color_vec.R

data-raw/config/KEGG_ID.csv

data-raw/config/Xlinked.tsv

data-raw/config/cell_cycle.csv

data-raw/config/cluster_invivo.csv

data-raw/config/cluster_names.csv

data-raw/config/date2CS.csv

data-raw/config/expanded_color.csv

data-raw/config/mural_polar.csv

data-raw/config/name_conversion.csv

data-raw/config/simplify_go_terms.csv

data-raw/config_template.R data-raw/csv_data.R data-raw/format_conf.R data-raw/lineage_markers.R

data/CT.rda

data/GOsimp.rda

data/KeggID.rda

data/TF.rda

data/cell_cycle.rda

data/color_scheme.rda

data/color_vec.rda

data/convert_name.rda

data/date2CS.rda

data/format_conf.rda

data/lineage_markers.rda

data/orders.rda

data/vivo_clust.rda

inst/python/BRGPLVM/.branching_tb_R.py.swp

inst/python/BRGPLVM/BRGP_class.py

inst/python/BRGPLVM/BRGP_main.py

inst/python/BRGPLVM/BRGP_utils.py

inst/python/BRGPLVM/ChangePoint.py

inst/python/BRGPLVM/__init__.py

inst/python/BRGPLVM/__pycache__/BRGP_class.cpython-36.pyc

inst/python/BRGPLVM/__pycache__/BRGP_main.cpython-36.pyc

inst/python/BRGPLVM/__pycache__/BRGP_utils.cpython-36.pyc

inst/python/BRGPLVM/__pycache__/ChangePoint.cpython-36.pyc

inst/python/BRGPLVM/branching_tb.py

inst/python/BRGPLVM/branching_tb_R.py

inst/python/BRGPLVM/kernel_choice.py

inst/python/BRGPLVM/main_train.py

inst/python/GPLVM/GrandPrix.py

inst/python/GPLVM/__init__.py

inst/python/GPLVM/periodicity.py

inst/python/GPLVM/tb_gplvm.py

inst/python/GPLVM/tb_predict.py

inst/python/STREAM/__pycache__/utils.cpython-37.pyc

inst/python/STREAM/fitting_prob.py

inst/python/STREAM/stream_GPLVM.py

inst/python/STREAM/utils.py

inst/python/clono/TF_cell.csv

inst/python/clono/__pycache__/cp_pipeline.cpython-38.pyc

inst/python/clono/__pycache__/organoid.cpython-38.pyc

inst/python/clono/combine_all.R inst/python/clono/combine_raw.R

inst/python/clono/cp_pipeline.py

inst/python/clono/get_clone.py

inst/python/clono/organoid.py

inst/python/clono/quantify.sh

inst/python/clono/quantify_all.sh

inst/python/clono/random_check.py

inst/python/clono/segment_background.cppipe

inst/python/clono/segment_clono.py

inst/python/clono/summarise.py

inst/python/imaging/__pycache__/cp_pipeline.cpython-38.pyc

inst/python/imaging/__pycache__/organoid.cpython-38.pyc

inst/python/imaging/__pycache__/read_lif.cpython-38.pyc

inst/python/imaging/__pycache__/trace_parent.cpython-38.pyc

inst/python/imaging/combine_raw.R

inst/python/imaging/cp_pipeline.py

inst/python/imaging/determine_thre.py

inst/python/imaging/fluorescence.py

inst/python/imaging/lif_to_tiff.py

inst/python/imaging/organoid.py

inst/python/imaging/quantify.sh

inst/python/imaging/read_lif.py

inst/python/imaging/segment_cyto.cppipe

inst/python/imaging/segment_cyto.py

inst/python/imaging/show_examples.py

inst/python/imaging/summarise.py

inst/python/imaging/trace_parent.py

manuscript/figureS5.py

revision/figureS5.py

revision/img_clono.R revision/img_quant.R revision/pseudotime/1GPLVM.R revision/pseudotime/2STREAM.R

revision/pseudotime/3BRGP.sh

revision/tableS.R

vignettes/.gitignore

vignettes/GPLVM.Rmd

vignettes/TB_trajectory.png

vignettes/WGCNA.Rmd vignettes/basic_analysis.Rmd vignettes/batch_correction.Rmd vignettes/cell_similarity.Rmd vignettes/pathway_analysis.Rmd

Yutong441/TBdev documentation built on Dec. 18, 2021, 8:22 p.m.

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Yutong441/TBdev
Infer a Trophoblast Developmental Trajectory

Files in Yutong441/TBdev
Infer a Trophoblast Developmental Trajectory

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Yutong441/TBdev Infer a Trophoblast Developmental Trajectory

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Yutong441/TBdev
Infer a Trophoblast Developmental Trajectory

Files in Yutong441/TBdev
Infer a Trophoblast Developmental Trajectory