Files in garber-lab/VDJChef
VDJChef for vdj analysis
.DS_Store
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/.DS_Store
R/barplot.R
R/data.R
R/embedding.R
R/heatmap.R
R/import.R
R/summary.R
R/violinplot.R
README.md
VDJChef.Rproj
data/seu_analyzed.rda
inst/.DS_Store
inst/extdata/.DS_Store
inst/extdata/1kcells-multi/.DS_Store
inst/extdata/1kcells-multi/analysis/clustering/graphclust/clusters.csv
inst/extdata/1kcells-multi/analysis/clustering/kmeans_10_clusters/clusters.csv
inst/extdata/1kcells-multi/analysis/clustering/kmeans_2_clusters/clusters.csv
inst/extdata/1kcells-multi/analysis/clustering/kmeans_3_clusters/clusters.csv
inst/extdata/1kcells-multi/analysis/clustering/kmeans_4_clusters/clusters.csv
inst/extdata/1kcells-multi/analysis/clustering/kmeans_5_clusters/clusters.csv
inst/extdata/1kcells-multi/analysis/clustering/kmeans_6_clusters/clusters.csv
inst/extdata/1kcells-multi/analysis/clustering/kmeans_7_clusters/clusters.csv
inst/extdata/1kcells-multi/analysis/clustering/kmeans_8_clusters/clusters.csv
inst/extdata/1kcells-multi/analysis/clustering/kmeans_9_clusters/clusters.csv
inst/extdata/1kcells-multi/analysis/diffexp/graphclust/differential_expression.csv
inst/extdata/1kcells-multi/analysis/diffexp/kmeans_10_clusters/differential_expression.csv
inst/extdata/1kcells-multi/analysis/diffexp/kmeans_2_clusters/differential_expression.csv
inst/extdata/1kcells-multi/analysis/diffexp/kmeans_3_clusters/differential_expression.csv
inst/extdata/1kcells-multi/analysis/diffexp/kmeans_4_clusters/differential_expression.csv
inst/extdata/1kcells-multi/analysis/diffexp/kmeans_5_clusters/differential_expression.csv
inst/extdata/1kcells-multi/analysis/diffexp/kmeans_6_clusters/differential_expression.csv
inst/extdata/1kcells-multi/analysis/diffexp/kmeans_7_clusters/differential_expression.csv
inst/extdata/1kcells-multi/analysis/diffexp/kmeans_8_clusters/differential_expression.csv
inst/extdata/1kcells-multi/analysis/diffexp/kmeans_9_clusters/differential_expression.csv
inst/extdata/1kcells-multi/analysis/pca/10_components/components.csv
inst/extdata/1kcells-multi/analysis/pca/10_components/dispersion.csv
inst/extdata/1kcells-multi/analysis/pca/10_components/features_selected.csv
inst/extdata/1kcells-multi/analysis/pca/10_components/projection.csv
inst/extdata/1kcells-multi/analysis/pca/10_components/variance.csv
inst/extdata/1kcells-multi/analysis/tsne/2_components/projection.csv
inst/extdata/1kcells-multi/analysis/umap/2_components/projection.csv
inst/extdata/1kcells-multi/sc5p_v2_hs_T_1k_multi_5gex_t_count_analysis.tar.gz
inst/extdata/1kcells-multi/sc5p_v2_hs_T_1k_multi_5gex_t_count_cloupe.cloupe
inst/extdata/1kcells-multi/sc5p_v2_hs_T_1k_multi_5gex_t_count_filtered_feature_bc_matrix.h5
inst/extdata/1kcells-multi/sc5p_v2_hs_T_1k_multi_5gex_t_count_filtered_feature_bc_matrix.tar.gz
inst/extdata/1kcells-multi/sc5p_v2_hs_T_1k_multi_5gex_t_count_metrics_summary.csv
inst/extdata/1kcells-multi/sc5p_v2_hs_T_1k_multi_5gex_t_count_molecule_info.h5
inst/extdata/1kcells-multi/sc5p_v2_hs_T_1k_multi_5gex_t_count_possorted_genome_bam.bam.bai
inst/extdata/1kcells-multi/sc5p_v2_hs_T_1k_multi_5gex_t_count_raw_feature_bc_matrix.h5
inst/extdata/1kcells-multi/sc5p_v2_hs_T_1k_multi_5gex_t_count_raw_feature_bc_matrix.tar.gz
inst/extdata/1kcells-multi/sc5p_v2_hs_T_1k_multi_5gex_t_web_summary.html
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_all_contig.bam.bai
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_all_contig.fasta
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_all_contig.fasta.fai
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_all_contig.fastq
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_all_contig_annotations.bed
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_all_contig_annotations.csv
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_clonotypes.csv
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_concat_ref.bam
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_concat_ref.bam.bai
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_concat_ref.fasta
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_concat_ref.fasta.fai
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_consensus.bam
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_consensus.bam.bai
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_consensus.fasta
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_consensus.fasta.fai
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_consensus_annotations.csv
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_filtered_contig.fasta
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_filtered_contig.fastq
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_filtered_contig_annotations.csv
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_vdj_contig_info.pb
inst/extdata/1kcells-multi/vdj_t/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_vloupe.vloupe
inst/extdata/sc5p_v2_hs_T_1k_multi_5gex_t_count_filtered_feature_bc_matrix.h5
inst/extdata/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_clonotypes.csv
inst/extdata/sc5p_v2_hs_T_1k_multi_5gex_t_vdj_t_filtered_contig_annotations.csv
man/VDJ_visualize.Rd
man/addTCR.Rd
man/getTCR.Rd
man/get_topclonotypes.Rd
man/plot_embed_clonotype.Rd
man/plot_heatmap_clonotypes.Rd
man/plot_tcr_violin.Rd
man/plot_violin.Rd
man/seu_analyzed.Rd
