Files in timothy-barry/sceptre
Analysis of Single-Cell CRISPR Screen Data
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/RcppExports.R
R/assign_grna_functions.R
R/association_testing_functions_v2.R
R/aux_functions.R
R/cellwise_qc_functs.R
R/check_functions.R
R/data.R
R/getters_and_setters.R
R/import_functs.R
R/medium_level_functs_v2.R
R/mixture_model_functs.R
R/neg_control_functions.R
R/ondisc_functs.R
R/pair_constructor_functs.R
R/pairwise_qc_functs.R
R/plotting_functions.R
R/precomputation_functions.R
R/preprocessing_functions.R
R/qq_plot_helpers.R
R/s4_analysis_functs_1.R
R/s4_analysis_functs_2.R
R/s4_class.R
R/s4_helpers.R
R/sceptre.R
R/test_functs.R
README.Rmd
README.md
_pkgdown.yml
data-raw/DATASET_gene_table.R
data/gene_position_data_frame_grch37.rda
data/gene_position_data_frame_grch38.rda
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/articles/calibration_check.png
docs/articles/discovery_analysis.png
docs/articles/grna_count_assignments.png
docs/articles/grna_count_distribution.png
docs/articles/index.html
docs/articles/install.html
docs/articles/pipeline_schematic.png
docs/articles/power_check.png
docs/articles/qc.png
docs/articles/sceptre.html
docs/authors.html
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docs/reference/plot_response_grna_target_pair.html
docs/reference/plot_run_calibration_check-1.png
docs/reference/plot_run_calibration_check.html
docs/reference/plot_run_discovery_analysis-1.png
docs/reference/plot_run_discovery_analysis.html
docs/reference/plot_run_power_check-1.png
docs/reference/plot_run_power_check.html
docs/reference/plot_run_qc-1.png
docs/reference/plot_run_qc.html
docs/reference/print-sceptre_object-method.html
docs/reference/read_ondisc_backed_sceptre_object.html
docs/reference/run_calibration_check.html
docs/reference/run_discovery_analysis.html
docs/reference/run_power_check.html
docs/reference/run_qc.html
docs/reference/sceptre-package-1.png
docs/reference/sceptre-package-10.png
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docs/reference/sceptre-package-8.png
docs/reference/sceptre-package-9.png
docs/reference/sceptre-package.html
docs/reference/set_analysis_parameters.html
docs/reference/write_outputs_to_directory.html
docs/search.json
docs/sitemap.xml
inst/CITATION
man/assign_grnas.Rd
man/construct_cis_pairs.Rd
man/construct_positive_control_pairs.Rd
man/construct_trans_pairs.Rd
man/figures/hex.jpg
man/gene_position_data_frame_grch38.Rd
man/get_grna_assignments.Rd
man/get_response_matrix.Rd
man/get_result.Rd
man/import_data.Rd
man/import_data_from_cellranger.Rd
man/import_data_from_parse.Rd
man/plot-sceptre_object-method.Rd
man/plot_assign_grnas.Rd
man/plot_covariates.Rd
man/plot_grna_count_distributions.Rd
man/plot_response_grna_target_pair.Rd
man/plot_run_calibration_check.Rd
man/plot_run_discovery_analysis.Rd
man/plot_run_power_check.Rd
man/plot_run_qc.Rd
man/print-sceptre_object-method.Rd
man/read_ondisc_backed_sceptre_object.Rd
man/run_calibration_check.Rd
man/run_discovery_analysis.Rd
man/run_power_check.Rd
man/run_qc.Rd
man/sceptre-package.Rd
man/set_analysis_parameters.Rd
man/write_outputs_to_directory.Rd
sceptre.Rproj
src/RcppExports.cpp
src/check_functions.cpp
src/compute_nb_size_param_functions.cpp
src/generate_samples_functions.cpp
src/low_level_distilled_test.cpp
src/low_level_full_test.cpp
src/mixture_functs.cpp
src/negative_control_functions.cpp
src/pair_construction_functs.cpp
src/pairwise_qc.cpp
src/shared_low_level_functions.cpp
src/shared_low_level_functions.h
src/sparse_matrix_functs.cpp
tests/testthat.R
tests/testthat/helper-mock-data.R
tests/testthat/test-assign_grnas.R
tests/testthat/test-aux_functions.R
tests/testthat/test-check_functions.R
tests/testthat/test-mock-data-functions.R
tests/testthat/test-plotting_functions.R
tests/testthat/test-preprocessing_functs.R
tests/testthat/test-run_qc.R
tests/testthat/test-s4_analysis_functs_1.R
tests/testthat/test-s4_analysis_functs_2.R
tests/testthat/test-s4_helpers.R
vignettes/.gitignore
vignettes/calibration_check.png
vignettes/discovery_analysis.png
vignettes/grna_count_assignments.png
vignettes/grna_count_distribution.png
vignettes/pipeline_schematic.png
vignettes/power_check.png
vignettes/qc.png
vignettes/sceptre.Rmd
vignettes/update_vignette.sh
