Files in keshav-motwani/scanalysis
Multi-Sample Visualization and Immune Repertoire Analysis Utilities for Single-Cell Data
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/annotate_cdr3.R
R/annotate_chain_count.R
R/annotate_clonotype_count.R
R/annotate_gex_qc.R
R/assign_clonotypes.R
R/cache.R
R/compute_evenness_profile.R
R/conversion.R
R/datasets.R
R/encode_identity_frequency.R
R/filter_ambient_barcode.R
R/filter_gex_outliers.R
R/filter_vdj_chain_count.R
R/get_assay_data.R
R/get_cell_features.R
R/io_10x.R
R/pipe.R
R/plot_barcode_qc.R
R/plot_feature_distributions.R
R/plot_feature_heatmap.R
R/plot_gex_qc.R
R/plot_pairwise_features.R
R/plot_reduced_dimensions.R
R/plot_vdj_qc.R
R/plot_volcano.R
R/select_top_de_genes.R
R/unnest_vdj.R
README.Rmd
README.md
_pkgdown.yml
docs/404.html
docs/LICENSE-text.html
docs/articles/conversion.html
docs/articles/index.html
docs/articles/preprocessing.html
docs/articles/preprocessing_files/figure-html/ambient_barcode_plot-1.png
docs/articles/preprocessing_files/figure-html/plot_qc-1.png
docs/articles/preprocessing_files/figure-html/plot_qc-2.png
docs/articles/preprocessing_files/figure-html/plot_qc-3.png
docs/articles/preprocessing_files/figure-html/plot_qc-4.png
docs/articles/preprocessing_files/figure-html/plot_qc-5.png
docs/articles/preprocessing_files/figure-html/plot_qc_post-1.png
docs/articles/preprocessing_files/figure-html/plot_qc_post-2.png
docs/articles/preprocessing_files/figure-html/plot_qc_post-3.png
docs/articles/preprocessing_files/figure-html/plot_qc_post-4.png
docs/articles/preprocessing_files/figure-html/plot_qc_post-5.png
docs/articles/scanalysis.html
docs/authors.html
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/annotate_ambient_profile.html
docs/reference/annotate_cdr3.html
docs/reference/annotate_chain_count.html
docs/reference/annotate_clonotype_count.html
docs/reference/annotate_n_cells_expr.html
docs/reference/annotate_n_genes_expr.html
docs/reference/annotate_pct_gene_set.html
docs/reference/annotate_pct_total_reads.html
docs/reference/annotate_total_umi_count.html
docs/reference/assign_clonotypes.html
docs/reference/cache.html
docs/reference/compute_evenness_profile_long.html
docs/reference/compute_evenness_profile_matrix.html
docs/reference/convert_identity_frequency_matrix_to_long.html
docs/reference/dot-encode_identity_frequency_matrix.html
docs/reference/dot-filter_ambient_barcode_cellranger.html
docs/reference/dot-filter_ambient_barcode_empty_drops.html
docs/reference/dot-filter_ambient_barcode_inflection.html
docs/reference/dot-filter_ambient_barcode_knee.html
docs/reference/dot-get_cell_annotations.html
docs/reference/dot-get_cell_features_assay.html
docs/reference/dot-get_cell_features_assay_explicit_exp.html
docs/reference/dot-get_cell_features_coldata.html
docs/reference/dot-get_cell_features_reduced_dimensions.html
docs/reference/dot-get_feature_annotations.html
docs/reference/dot-get_reduced_dims.html
docs/reference/dot-prepare_barcode_counts.html
docs/reference/dot-prepare_barcode_cutoffs.html
docs/reference/dot-prepare_barcode_plot_data.html
docs/reference/dot-prepare_gex_bivariate_counts.html
docs/reference/dot-prepare_gex_data.html
docs/reference/dot-prepare_gex_scale_limits.html
docs/reference/dot-prepare_gex_univariate_counts.html
docs/reference/dot-prepare_volcano_annotations.html
docs/reference/dot-read_10x_gene_expr.html
docs/reference/dot-read_10x_vdj.html
docs/reference/dot-sce_to_assay.html
docs/reference/dot-seurat_assay_to_sce.html
docs/reference/encode_cell_identity_frequency_long.html
docs/reference/encode_cell_identity_frequency_matrix.html
docs/reference/encode_vdj_identity_frequency_long.html
docs/reference/encode_vdj_identity_frequency_matrix.html
docs/reference/example_data/17d2933b3fdf5_5k_pbmc_v3_filtered_feature_bc_matrix.tar.gz
docs/reference/example_data/17d296aadba92_5k_pbmc_v3_nextgem_filtered_feature_bc_matrix.tar.gz
docs/reference/example_data/BiocFileCache.sqlite
docs/reference/example_data/pbmc_5k_nextgem/filtered_feature_bc_matrix/barcodes.tsv.gz
docs/reference/example_data/pbmc_5k_nextgem/filtered_feature_bc_matrix/features.tsv.gz
docs/reference/example_data/pbmc_5k_nextgem/filtered_feature_bc_matrix/matrix.mtx.gz
docs/reference/example_data/pbmc_5k_v3/filtered_feature_bc_matrix/barcodes.tsv.gz
docs/reference/example_data/pbmc_5k_v3/filtered_feature_bc_matrix/features.tsv.gz
docs/reference/example_data/pbmc_5k_v3/filtered_feature_bc_matrix/matrix.mtx.gz
docs/reference/filter_ambient_barcode.html
docs/reference/filter_n_genes_expr.html
docs/reference/filter_pct_mito.html
docs/reference/filter_total_umi.html
docs/reference/filter_vdj_chain_count.html
docs/reference/get_assay_data.html
docs/reference/get_cell_features.html
docs/reference/get_multi_sample_pbmc_10k.html
docs/reference/get_pbmc_5k_nextgem.html
docs/reference/get_pbmc_5k_v3.html
docs/reference/get_row_data.html
docs/reference/index.html
docs/reference/pipe.html
docs/reference/plot_barcode_qc.html
docs/reference/plot_feature_distributions.html
docs/reference/plot_feature_heatmap.html
docs/reference/plot_gex_bivariate_qc.html
docs/reference/plot_gex_univariate_qc.html
docs/reference/plot_pairwise_features.html
docs/reference/plot_reduced_dimensions.html
docs/reference/plot_vdj_gex_univariate_qc.html
docs/reference/plot_volcano.html
docs/reference/read_10x.html
docs/reference/sce_to_seurat.html
docs/reference/select_top_de_genes.html
docs/reference/seurat_to_sce.html
docs/reference/unnest_vdj.html
man/annotate_ambient_profile.Rd
man/annotate_cdr3.Rd
man/annotate_chain_count.Rd
man/annotate_clonotype_count.Rd
man/annotate_n_cells_expr.Rd
man/annotate_n_genes_expr.Rd
man/annotate_pct_gene_set.Rd
man/annotate_pct_total_reads.Rd
man/annotate_total_umi_count.Rd
man/assign_clonotypes.Rd
man/cache.Rd
man/compute_evenness_profile_long.Rd
man/compute_evenness_profile_matrix.Rd
man/convert_identity_frequency_matrix_to_long.Rd
man/dot-encode_identity_frequency_matrix.Rd
man/dot-filter_ambient_barcode_cellranger.Rd
man/dot-filter_ambient_barcode_empty_drops.Rd
man/dot-filter_ambient_barcode_inflection.Rd
man/dot-filter_ambient_barcode_knee.Rd
man/dot-get_cell_annotations.Rd
man/dot-get_cell_features_assay.Rd
man/dot-get_cell_features_assay_explicit_exp.Rd
man/dot-get_cell_features_coldata.Rd
man/dot-get_cell_features_reduced_dimensions.Rd
man/dot-get_feature_annotations.Rd
man/dot-get_reduced_dims.Rd
man/dot-prepare_barcode_counts.Rd
man/dot-prepare_barcode_cutoffs.Rd
man/dot-prepare_barcode_plot_data.Rd
man/dot-prepare_gex_bivariate_counts.Rd
man/dot-prepare_gex_data.Rd
man/dot-prepare_gex_scale_limits.Rd
man/dot-prepare_gex_univariate_counts.Rd
man/dot-prepare_volcano_annotations.Rd
man/dot-read_10x_gene_expr.Rd
man/dot-read_10x_vdj.Rd
man/dot-sce_to_assay.Rd
man/dot-seurat_assay_to_sce.Rd
man/encode_cell_identity_frequency_long.Rd
man/encode_cell_identity_frequency_matrix.Rd
man/encode_vdj_identity_frequency_long.Rd
man/encode_vdj_identity_frequency_matrix.Rd
man/filter_ambient_barcode.Rd
man/filter_n_genes_expr.Rd
man/filter_pct_mito.Rd
man/filter_total_umi.Rd
man/filter_vdj_chain_count.Rd
man/get_assay_data.Rd
man/get_cell_features.Rd
man/get_multi_sample_pbmc_10k.Rd
man/get_pbmc_5k_nextgem.Rd
man/get_pbmc_5k_v3.Rd
man/get_row_data.Rd
man/pipe.Rd
man/plot_barcode_qc.Rd
man/plot_feature_distributions.Rd
man/plot_feature_heatmap.Rd
man/plot_gex_bivariate_qc.Rd
man/plot_gex_univariate_qc.Rd
man/plot_pairwise_features.Rd
man/plot_reduced_dimensions.Rd
man/plot_vdj_gex_univariate_qc.Rd
man/plot_volcano.Rd
man/read_10x.Rd
man/sce_to_seurat.Rd
man/select_top_de_genes.Rd
man/seurat_to_sce.Rd
man/unnest_vdj.Rd
scanalysis.Rproj
tests/testthat.R
tests/testthat/test_encode_identity_frequency.R
tests/testthat/toy_data.rds
vignettes/.gitignore
vignettes/conversion.Rmd
vignettes/preprocessing.Rmd
