tests/testthat/_snaps/project.md
In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language
project initialization and update works
Code
list.files(recursive = TRUE)
Output
[1] "Rmd/common/_footer.Rmd"
[2] "Rmd/common/_header.Rmd"
[3] "Rmd/common/cluster_markers.Rmd"
[4] "Rmd/common/cluster_markers_table_template.Rmd"
[5] "Rmd/common/clustering/cluster_graph_leiden.Rmd"
[6] "Rmd/common/clustering/cluster_graph_louvain.Rmd"
[7] "Rmd/common/clustering/cluster_graph_walktrap.Rmd"
[8] "Rmd/common/clustering/cluster_kmeans.Rmd"
[9] "Rmd/common/clustering/cluster_sc3.Rmd"
[10] "Rmd/common/clustering/clustering.Rmd"
[11] "Rmd/common/contrasts.Rmd"
[12] "Rmd/common/contrasts_table_template.Rmd"
[13] "Rmd/common/stylesheet.css"
[14] "Rmd/integration/01_integration.Rmd"
[15] "Rmd/integration/02_int_clustering.Rmd"
[16] "Rmd/single_sample/01_input_qc.Rmd"
[17] "Rmd/single_sample/01_input_qc_children/cell_filtering_custom.Rmd"
[18] "Rmd/single_sample/01_input_qc_children/cell_filtering_qc.Rmd"
[19] "Rmd/single_sample/01_input_qc_children/empty_droplets.Rmd"
[20] "Rmd/single_sample/01_input_qc_children/gene_filtering_custom.Rmd"
[21] "Rmd/single_sample/01_input_qc_children/gene_filtering_qc.Rmd"
[22] "Rmd/single_sample/02_norm_clustering.Rmd"
[23] "Rmd/single_sample/02_norm_clustering_simple.Rmd"
[24] "_drake_integration.R"
[25] "_drake_single_sample.R"
[26] "config/integration/00_main.default.yaml"
[27] "config/integration/00_main.yaml"
[28] "config/integration/01_integration.default.yaml"
[29] "config/integration/01_integration.yaml"
[30] "config/integration/02_int_clustering.default.yaml"
[31] "config/integration/02_int_clustering.yaml"
[32] "config/integration/cluster_markers.default.yaml"
[33] "config/integration/cluster_markers.yaml"
[34] "config/integration/contrasts.default.yaml"
[35] "config/integration/contrasts.yaml"
[36] "config/pipeline.default.yaml"
[37] "config/pipeline.yaml"
[38] "config/single_sample/00_main.default.yaml"
[39] "config/single_sample/00_main.yaml"
[40] "config/single_sample/01_input_qc.default.yaml"
[41] "config/single_sample/01_input_qc.yaml"
[42] "config/single_sample/02_norm_clustering.default.yaml"
[43] "config/single_sample/02_norm_clustering.yaml"
[44] "config/single_sample/cluster_markers.default.yaml"
[45] "config/single_sample/cluster_markers.yaml"
[46] "config/single_sample/contrasts.default.yaml"
[47] "config/single_sample/contrasts.yaml"
[48] "plan_custom.R"
[49] "renv.lock"
[50] "selected_markers.csv"
Code
list.files(recursive = TRUE)
Output
[1] "Rmd/common/_footer.Rmd"
[2] "Rmd/common/_header.Rmd"
[3] "Rmd/common/cluster_markers.Rmd"
[4] "Rmd/common/cluster_markers_table_template.Rmd"
[5] "Rmd/common/clustering/cluster_graph_leiden.Rmd"
[6] "Rmd/common/clustering/cluster_graph_louvain.Rmd"
[7] "Rmd/common/clustering/cluster_graph_walktrap.Rmd"
[8] "Rmd/common/clustering/cluster_kmeans.Rmd"
[9] "Rmd/common/clustering/cluster_sc3.Rmd"
[10] "Rmd/common/clustering/clustering.Rmd"
[11] "Rmd/common/contrasts.Rmd"
[12] "Rmd/common/contrasts_table_template.Rmd"
[13] "Rmd/common/stylesheet.css"
[14] "Rmd/integration/01_integration.Rmd"
[15] "Rmd/integration/02_int_clustering.Rmd"
[16] "Rmd/single_sample/01_input_qc.Rmd"
[17] "Rmd/single_sample/01_input_qc_children/cell_filtering_custom.Rmd"
[18] "Rmd/single_sample/01_input_qc_children/cell_filtering_qc.Rmd"
[19] "Rmd/single_sample/01_input_qc_children/empty_droplets.Rmd"
[20] "Rmd/single_sample/01_input_qc_children/gene_filtering_custom.Rmd"
[21] "Rmd/single_sample/01_input_qc_children/gene_filtering_qc.Rmd"
[22] "Rmd/single_sample/02_norm_clustering.Rmd"
[23] "Rmd/single_sample/02_norm_clustering_simple.Rmd"
[24] "_drake_integration.R"
[25] "_drake_single_sample.R"
[26] "config/integration/00_main.default.yaml"
[27] "config/integration/00_main.yaml"
[28] "config/integration/00_main.yaml.backup"
[29] "config/integration/01_integration.default.yaml"
[30] "config/integration/01_integration.yaml"
[31] "config/integration/01_integration.yaml.backup"
[32] "config/integration/02_int_clustering.default.yaml"
[33] "config/integration/02_int_clustering.yaml"
[34] "config/integration/02_int_clustering.yaml.backup"
[35] "config/integration/cluster_markers.default.yaml"
[36] "config/integration/cluster_markers.yaml"
[37] "config/integration/cluster_markers.yaml.backup"
[38] "config/integration/contrasts.default.yaml"
[39] "config/integration/contrasts.yaml"
[40] "config/integration/contrasts.yaml.backup"
[41] "config/pipeline.default.yaml"
[42] "config/pipeline.yaml"
[43] "config/pipeline.yaml.backup"
[44] "config/single_sample/00_main.default.yaml"
[45] "config/single_sample/00_main.yaml"
[46] "config/single_sample/00_main.yaml.backup"
[47] "config/single_sample/01_input_qc.default.yaml"
[48] "config/single_sample/01_input_qc.yaml"
[49] "config/single_sample/01_input_qc.yaml.backup"
[50] "config/single_sample/02_norm_clustering.default.yaml"
[51] "config/single_sample/02_norm_clustering.yaml"
[52] "config/single_sample/02_norm_clustering.yaml.backup"
[53] "config/single_sample/cluster_markers.default.yaml"
[54] "config/single_sample/cluster_markers.yaml"
[55] "config/single_sample/cluster_markers.yaml.backup"
[56] "config/single_sample/contrasts.default.yaml"
[57] "config/single_sample/contrasts.yaml"
[58] "config/single_sample/contrasts.yaml.backup"
[59] "plan_custom.R"
[60] "plan_custom.orig.R"
[61] "renv.lock"
[62] "selected_markers.csv"
bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
project initialization and update works
Code
list.files(recursive = TRUE)
Output
[1] "Rmd/common/_footer.Rmd"
[2] "Rmd/common/_header.Rmd"
[3] "Rmd/common/cluster_markers.Rmd"
[4] "Rmd/common/cluster_markers_table_template.Rmd"
[5] "Rmd/common/clustering/cluster_graph_leiden.Rmd"
[6] "Rmd/common/clustering/cluster_graph_louvain.Rmd"
[7] "Rmd/common/clustering/cluster_graph_walktrap.Rmd"
[8] "Rmd/common/clustering/cluster_kmeans.Rmd"
[9] "Rmd/common/clustering/cluster_sc3.Rmd"
[10] "Rmd/common/clustering/clustering.Rmd"
[11] "Rmd/common/contrasts.Rmd"
[12] "Rmd/common/contrasts_table_template.Rmd"
[13] "Rmd/common/stylesheet.css"
[14] "Rmd/integration/01_integration.Rmd"
[15] "Rmd/integration/02_int_clustering.Rmd"
[16] "Rmd/single_sample/01_input_qc.Rmd"
[17] "Rmd/single_sample/01_input_qc_children/cell_filtering_custom.Rmd"
[18] "Rmd/single_sample/01_input_qc_children/cell_filtering_qc.Rmd"
[19] "Rmd/single_sample/01_input_qc_children/empty_droplets.Rmd"
[20] "Rmd/single_sample/01_input_qc_children/gene_filtering_custom.Rmd"
[21] "Rmd/single_sample/01_input_qc_children/gene_filtering_qc.Rmd"
[22] "Rmd/single_sample/02_norm_clustering.Rmd"
[23] "Rmd/single_sample/02_norm_clustering_simple.Rmd"
[24] "_drake_integration.R"
[25] "_drake_single_sample.R"
[26] "config/integration/00_main.default.yaml"
[27] "config/integration/00_main.yaml"
[28] "config/integration/01_integration.default.yaml"
[29] "config/integration/01_integration.yaml"
[30] "config/integration/02_int_clustering.default.yaml"
[31] "config/integration/02_int_clustering.yaml"
[32] "config/integration/cluster_markers.default.yaml"
[33] "config/integration/cluster_markers.yaml"
[34] "config/integration/contrasts.default.yaml"
[35] "config/integration/contrasts.yaml"
[36] "config/pipeline.default.yaml"
[37] "config/pipeline.yaml"
[38] "config/single_sample/00_main.default.yaml"
[39] "config/single_sample/00_main.yaml"
[40] "config/single_sample/01_input_qc.default.yaml"
[41] "config/single_sample/01_input_qc.yaml"
[42] "config/single_sample/02_norm_clustering.default.yaml"
[43] "config/single_sample/02_norm_clustering.yaml"
[44] "config/single_sample/cluster_markers.default.yaml"
[45] "config/single_sample/cluster_markers.yaml"
[46] "config/single_sample/contrasts.default.yaml"
[47] "config/single_sample/contrasts.yaml"
[48] "plan_custom.R"
[49] "renv.lock"
[50] "selected_markers.csv"
Code
list.files(recursive = TRUE)
Output
[1] "Rmd/common/_footer.Rmd"
[2] "Rmd/common/_header.Rmd"
[3] "Rmd/common/cluster_markers.Rmd"
[4] "Rmd/common/cluster_markers_table_template.Rmd"
[5] "Rmd/common/clustering/cluster_graph_leiden.Rmd"
[6] "Rmd/common/clustering/cluster_graph_louvain.Rmd"
[7] "Rmd/common/clustering/cluster_graph_walktrap.Rmd"
[8] "Rmd/common/clustering/cluster_kmeans.Rmd"
[9] "Rmd/common/clustering/cluster_sc3.Rmd"
[10] "Rmd/common/clustering/clustering.Rmd"
[11] "Rmd/common/contrasts.Rmd"
[12] "Rmd/common/contrasts_table_template.Rmd"
[13] "Rmd/common/stylesheet.css"
[14] "Rmd/integration/01_integration.Rmd"
[15] "Rmd/integration/02_int_clustering.Rmd"
[16] "Rmd/single_sample/01_input_qc.Rmd"
[17] "Rmd/single_sample/01_input_qc_children/cell_filtering_custom.Rmd"
[18] "Rmd/single_sample/01_input_qc_children/cell_filtering_qc.Rmd"
[19] "Rmd/single_sample/01_input_qc_children/empty_droplets.Rmd"
[20] "Rmd/single_sample/01_input_qc_children/gene_filtering_custom.Rmd"
[21] "Rmd/single_sample/01_input_qc_children/gene_filtering_qc.Rmd"
[22] "Rmd/single_sample/02_norm_clustering.Rmd"
[23] "Rmd/single_sample/02_norm_clustering_simple.Rmd"
[24] "_drake_integration.R"
[25] "_drake_single_sample.R"
[26] "config/integration/00_main.default.yaml"
[27] "config/integration/00_main.yaml"
[28] "config/integration/00_main.yaml.backup"
[29] "config/integration/01_integration.default.yaml"
[30] "config/integration/01_integration.yaml"
[31] "config/integration/01_integration.yaml.backup"
[32] "config/integration/02_int_clustering.default.yaml"
[33] "config/integration/02_int_clustering.yaml"
[34] "config/integration/02_int_clustering.yaml.backup"
[35] "config/integration/cluster_markers.default.yaml"
[36] "config/integration/cluster_markers.yaml"
[37] "config/integration/cluster_markers.yaml.backup"
[38] "config/integration/contrasts.default.yaml"
[39] "config/integration/contrasts.yaml"
[40] "config/integration/contrasts.yaml.backup"
[41] "config/pipeline.default.yaml"
[42] "config/pipeline.yaml"
[43] "config/pipeline.yaml.backup"
[44] "config/single_sample/00_main.default.yaml"
[45] "config/single_sample/00_main.yaml"
[46] "config/single_sample/00_main.yaml.backup"
[47] "config/single_sample/01_input_qc.default.yaml"
[48] "config/single_sample/01_input_qc.yaml"
[49] "config/single_sample/01_input_qc.yaml.backup"
[50] "config/single_sample/02_norm_clustering.default.yaml"
[51] "config/single_sample/02_norm_clustering.yaml"
[52] "config/single_sample/02_norm_clustering.yaml.backup"
[53] "config/single_sample/cluster_markers.default.yaml"
[54] "config/single_sample/cluster_markers.yaml"
[55] "config/single_sample/cluster_markers.yaml.backup"
[56] "config/single_sample/contrasts.default.yaml"
[57] "config/single_sample/contrasts.yaml"
[58] "config/single_sample/contrasts.yaml.backup"
[59] "plan_custom.R"
[60] "plan_custom.orig.R"
[61] "renv.lock"
[62] "selected_markers.csv"
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