Files in Jorisvansteenbrugge/TcT
Trait-based Comparative Transcriptomics
.Rbuildignore
.gitignore
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
R/Calc_Pairwise_Annotation_Distance.R
R/Calc_Z_scores.R
R/Identify_Trait_Attributes.R
R/Individual_Annotation_Background.R
R/Prune_Trait_Attributes.R
R/Random_Trait_Background.R
R/Significance_Trait.R
R/Utility.R
R/Wrapper.R
R/benchmarking/.benchmark_low_coverage.R.swp
R/benchmarking/benchmark_low_coverage.R
R/benchmarking/benchmark_low_coverage_interpretation.R
R/benchmarking/benchmark_zero_counts_genewise.R
R/benchmarking/benchmark_zero_counts_genewise_interpretation.R
R/dont_run.Rmd
R/preprocess.R
R/random things.R
R/zzz.R
README.md
Rplot.png
TbasCO.Rproj
data/Custom_modules.tsv
data/KEGG_modules_deprecated.tsv
data/KO_identifiers.keg
data/KO_identifiers.keg.bak
data/brite/20191208_kegg_brite_secretion_systems.keg
data/brite/20191208_kegg_brite_transporters.keg
data/brite/20191208_kegg_brite_two_component.keg
data/brite/2020_05_kegg_brite_secretion_systems.json
data/brite/2020_05_kegg_brite_transporters.json
data/brite/2020_05_kegg_brite_two_component_systems.json
data/brite/attribute_list_secretion_twocomp_transporter.csv
data/cytoscape_tables/attribute_list_combined.csv
data/cytoscape_tables/attribute_list_modules.csv
data/cytoscape_tables/expanded_attribute_table.csv
data/get_module_categories.py
data/kegg_brite_20191208_db.RData
data/kegg_categories_2020_05.json
data/kegg_module_2019_07_23.RData
data/kegg_module_attribute_list.tsv
data/kegg_modules_2019_07_23.tsv
data/kegg_modules_2019_07_23_DNF_flat.tsv
data/ko_term_dump.txt
data/module_categories.RData
data/sample_data.csv
data/sub_modules.RData
docs/_config.yml
docs/about.md
docs/index.md
docs/mkdocs.yml
docs/test.md
kegg_modules_2019_07_23.tsv
man/Add-Custom-Trait.Rd
man/Calc_Z_scores.Rd
man/Calculate-Association-Rules.Rd
man/Create.Rank.Columns.Rd
man/Create_Filtered_SBS_Matrix.Rd
man/Draw-Expression.Rd
man/Filter.Rd
man/GetTraitAttributes.Rd
man/Get_annotation_presence_absence.Rd
man/Get_matrix_features.Rd
man/Get_module_categories.Rd
man/Go-Fish.Rd
man/Identify-Trait-Attributes.Rd
man/Identify_Significance_Trait.Rd
man/Individual-Random-Background-distributions.Rd
man/Model_Module.Rd
man/Normalization.Rd
man/Normalize.Rd
man/Pairwise-comparison-of-Annotations.Rd
man/Plot-Background-Individual-Genes.Rd
man/Plot-Background-Modules.Rd
man/Plot-Metric-Comparison.Rd
man/Plot-Trait-Attribute.Rd
man/Plot_Model_Module.Rd
man/Plot_Redundancy_Traits.Rd
man/Pre_process_input.Rd
man/Prune-Trait-Attributes.Rd
man/Random-Background-distributions-of-Traits.Rd
man/Random.Annotated.Genes.bkgd.Rd
man/Random.Genes.bkgd.Rd
man/Random.Identical.Annotated.Genes.bkgd.Rd
man/getMetricDist.Rd
man/getMetricDistModule.Rd
man/gradient.legend.Rd
man/number.to.colors.Rd
man/string.to.colors.Rd
python/brite_parse.py
python/expand_attribute_list.py
python/generate_kegg_attribute_list.py
python/generate_kegg_brite_attribute_list.py
python/module_parse.py
python/parse_module_definition.py
python/tmp_ko00002_2019_7_23.keg
tests/testthat.R
tests/testthat/test_PHA.R
tests/testthat/test_filter.R
tests/testthat/test_normrank.R
tests/testthat/test_trait_PA.R
vignettes/Custom_Traits.Rmd
vignettes/Custom_Traits.nb.html
vignettes/EBPR.Rmd
vignettes/EBPR_messing_around.Rmd
vignettes/basic.Rmd
