Files in philippmuench/OligoMMR
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
OligoMMR.Rproj
R/coverage.R
R/heatmaps.R
R/helpers.R
README.md
data-raw/Acutalibacter_muris_KB18_covereage.rds
data-raw/Akkermansia_muciniphila_YL44_covereage.rds
data-raw/Bacteroides_caecimuris_I48_coverage.rds
data-raw/Bifidobacterium_animalis_YL2_covereage.rds
data-raw/Blautia_coccoides_YL58_coverage.rds
data-raw/Clostridium_innocuum_I46_coverage.rds
data-raw/Enterococcus_faecalis_KB1_coverage.rds
data-raw/Flavonifractor_plautii_YL31_coverage.rds
data-raw/Limosilactobacillus_reuteri_I49_coverage.rds
data-raw/Muribaculum_intestinale_YL27_coverage.rds
data-raw/omm_ab_isolates.R
data-raw/omm_ab_isolates.rds
data-raw/omm_ab_isolates_corrected.R
data-raw/omm_ab_isolates_corrected.rds
data-raw/omm_ab_wgs.R
data-raw/omm_ab_wgs.rds
data-raw/omm_ab_wgs_imputed_long.R
data-raw/omm_ab_wgs_imputed_wide.R
data-raw/omm_wgs_imputed_long_filtered.rds
data-raw/omm_wgs_imputed_wide_filtered.rds
data/oligomm_ab_coverage_Acutalibacter_muris_KB18.rda
data/oligomm_ab_coverage_Akkermansia_muciniphila_YL44.rda
data/oligomm_ab_coverage_Bacteroides_caecimuris_I48.rda
data/oligomm_ab_coverage_Bifidobacterium_animalis_YL2.rda
data/oligomm_ab_coverage_Blautia_coccoides_YL58.rda
data/oligomm_ab_coverage_Clostridium_innocuum_I46.rda
data/oligomm_ab_coverage_Enterocloster_clostridioformis_YL32.rda
data/oligomm_ab_coverage_Enterocloster_clostridioformis_YL32_covereage.rda
data/oligomm_ab_coverage_Enterococcus_faecalis_KB1.rda
data/oligomm_ab_coverage_Flavonifractor_plautii_YL31.rda
data/oligomm_ab_coverage_Limosilactobacillus_reuteri_I49.rda
data/oligomm_ab_coverage_Muribaculum_intestinale_YL27.rda
data/oligomm_ab_isolates.rda
data/oligomm_ab_isolates_corrected.rda
data/oligomm_ab_mic.rda
data/oligomm_ab_mic_community.rda
data/oligomm_ab_phages_phaster_incomplete.rda
data/oligomm_ab_phages_phaster_intact.rda
data/oligomm_ab_wgs.rda
data/oligomm_ab_wgs_imputed_long.rda
data/oligomm_ab_wgs_imputed_wide.rda
inst/.DS_Store
inst/rmd/Figure5_duplication.Rmd
inst/rmd/Figure5_duplication.nb.html
inst/rmd/Figure_1.Rmd
inst/rmd/Figure_2.Rmd
inst/rmd/Figure_2.html
inst/rmd/Figure_3.Rmd
inst/rmd/Figure_3_a.pdf
inst/rmd/Figure_3_b.pdf
inst/rmd/Figure_4.Rmd
inst/rmd/Figure_4_B.pdf
inst/rmd/Figure_4_a.pdf
inst/rmd/Figure_4_c.pdf
inst/rmd/Figure_4_d.pdf
inst/rmd/Figure_4_e.pdf
inst/rmd/Figure_5.Rmd
inst/rmd/Figure_5.html
inst/rmd/Figure_S1.Rmd
inst/rmd/Figure_S1.html
inst/rmd/Figure_S2.Rmd
inst/rmd/Figure_SX1.Rmd
inst/rmd/Figure_SX1.pdf
inst/rmd/Figure_SX1_2.pdf
inst/rmd/Figure_SX2.pdf
inst/rmd/figure5_corrected.pdf
inst/rmd/pdf/figure5.pdf
inst/rmd/pdf/figure5_dend.pdf
inst/rmd/pdf/figure5_dend_b_co.pdf
inst/rmd/pdf/figure_5_panel_c.pdf
inst/rmd/pdf/hclust.pdf
inst/rmd/phage1_Bacteroides_caecimuris_I48.pdf
man/binDaysByPhase.Rd
man/binDaysByPhaseGroup.Rd
man/create_heatmap_iso.Rd
man/group2color.Rd
man/theme_pmuench.Rd
man/translateGenomeIdToFullName.Rd
man/translateIsolateIDtoBug.Rd
man/translateIsolateIDtoMouse.Rd
man/translateMouseIdToABC.Rd
man/translateMouseIdToTreatmentGroup.Rd
