Chapter 3 Quality Control
Loading packages
library(XMAS2)
library(dplyr)
library(tibble)
library(phyloseq)The taxonomic levels of spike-in sample’s bacteria is species. Firstly, using the summarize_taxa to get the species level phyloseq object and then do run_RefCheck under the optimal parameters.
3.1 spike-in sample (BRS)
- get the BRS_ID
metaphlan2_ps_LOD_species <- aggregate_LOD_taxa(ps = metaphlan2_ps,
taxa_level = "Species",
cutoff = 1e-04)
metaphlan2_ps_LOD_species@sam_data## Group phynotype
## s1 BB 0.00
## s2 AA 2.50
## s3 BB 0.00
## s4 AA 1.25
## s5 AA 30.00
## s6 AA 15.00
## s7 BB 8.75
## s8 BB 0.00
## s9 BB 3.75
## s10 BB 2.50
## s11 BB 15.00
## s12 BB 2.50
## s13 BB 2.50
## s14 BB 0.00
## s15 BB 1.07
## s16 BB 2.50
## s17 AA 5.00
## s18 BB 35.00
## s19 BB 7.50
## s20 BB 15.00
## s21 AA 3.75
## s22 AA 3.75
## refE QC NA- run
run_RefCheck
run_RefCheck(
ps = metaphlan2_ps_LOD_species,
BRS_ID = "refE",
Ref_type = "MGS")## Noting: the Reference Matrix is for MGS
##
## ############Matched baterica of the BRS sample#############
## The number of BRS' bacteria matched the Reference Matrix is [16]
## s__Bifidobacterium_longum
## s__Bacteroides_ovatus
## s__Coprococcus_comes
## s__Bacteroides_vulgatus
## s__Bifidobacterium_adolescentis
## s__Bacteroides_thetaiotaomicron
## s__Streptococcus_salivarius
## s__Dorea_formicigenerans
## s__Bifidobacterium_pseudocatenulatum
## s__Bacteroides_uniformis
## s__Bacteroides_xylanisolvens
## s__Prevotella_copri
## s__Faecalibacterium_prausnitzii
## s__Collinsella_aerofaciens
## s__Lachnospiraceae_bacterium_5_1_63FAA
## s__Roseburia_hominis
## The number of bacteria unmatched the Reference Matrix is [11]
## s__Enterococcus_faecalis
## s__Escherichia_coli
## s__Bacteroides_fragilis
## s__Parabacteroides_goldsteinii
## s__Lactobacillus_salivarius
## s__Enterococcus_faecium
## s__Bifidobacterium_bifidum
## s__Lactobacillus_pentosus
## s__Eggerthella_unclassified
## s__Propionibacterium_acnes
## s__Bacteroides_intestinalis
## The number of the additional bacteria compared to the Reference Matrix is [44]
## ###########################################################
##
## ##################Status of the BRS sample##################
## Whether the BRS has the all bateria of Reference Matrix: FALSE
## Correlation Coefficient of the BRS is: -0.04118
## Bray Curtis of the BRS is: 0.8735
## Impurity of the BRS is: 32.69
## ###########################################################
## #####Final Evaluation Results of the BRS #######
## The BRS of sequencing dataset didn't pass the cutoff of the Reference Matrix
## ###########################################################
## 10471 10636 10637 10639 10640 10769 11115 11708 12592 13164 13331
## Bifidobacterium_longum 8.11381 7.67316 7.50927 5.70807 4.86413 11.54558 13.32375 12.83483 8.31626 12.25656 11.64168
## Bacteroides_ovatus 3.96168 3.92905 3.86741 4.44106 4.15994 2.99928 2.88927 2.74802 3.05585 2.78285 2.30211
## Coprococcus_comes 4.16280 4.18702 4.65603 4.40718 5.15653 1.73091 1.44618 1.57966 1.78718 1.34019 1.50536
## Bacteroides_vulgatus 3.35465 3.47741 3.43735 4.01041 3.92425 2.84171 2.73213 2.52132 3.08322 2.66631 2.21000
## Bifidobacterium_adolescentis 5.11369 5.10202 5.16323 3.75219 3.55822 7.14673 7.12725 7.89869 5.49066 6.57327 8.94479
## Bacteroides_thetaiotaomicron 3.24092 3.21696 3.20104 3.49194 3.50958 2.97032 3.00366 2.75088 3.22968 2.92743 2.43185
## Streptococcus_salivarius 3.03030 2.85413 2.95267 2.96550 3.04982 3.35350 3.15495 3.10234 3.62476 3.37613 3.44728
## Dorea_formicigenerans 2.79346 2.77945 2.91141 2.75671 3.01534 5.81678 4.69992 4.59889 5.74800 4.69777 5.32816
## Bifidobacterium_pseudocatenulatum 3.38286 3.16577 3.07946 2.67246 2.40422 7.49415 8.06924 6.93314 5.83010 7.11283 6.83227
## Bacteroides_uniformis 2.69622 2.41265 2.41435 2.59011 2.40581 1.73867 2.27891 1.82426 1.99951 1.96071 1.83481
## Bacteroides_xylanisolvens 3.28194 3.29517 1.72138 2.23987 3.72633 3.04333 1.36887 2.58554 2.99954 1.36453 2.31131
## Prevotella_copri 2.06364 1.82281 1.87249 1.93086 1.88097 1.91383 1.81769 1.79535 1.84980 1.93870 1.88402
## Faecalibacterium_prausnitzii 0.77201 0.75578 0.79594 0.37908 0.35665 0.63169 0.86543 0.87373 0.37657 0.73631 0.78754
## Collinsella_aerofaciens 0.53383 0.49729 0.50462 0.30319 0.25888 0.58329 0.82169 0.84559 0.41288 0.77006 0.75924
## Lachnospiraceae_bacterium_5_1_63FAA 0.08820 0.10673 0.11128 0.10783 0.16420 0.16237 0.09083 0.09210 0.15412 0.08988 0.14991
## Roseburia_hominis 0.06173 0.05838 0.06817 0.05414 0.04661 0.04053 0.05378 0.04942 0.04577 0.04584 0.04223
## 13837 13864 13883 14294 14353 14514 14692 15043 15377 15378 15919
## Bifidobacterium_longum 12.64388 11.36085 9.62482 14.35451 16.63263 9.93664 9.47707 7.11444 10.55997 9.07591 10.01176
## Bacteroides_ovatus 3.17694 2.66994 3.27074 2.79573 2.87388 2.76674 3.46729 3.61227 3.49421 3.03110 2.76744
## Coprococcus_comes 1.50964 2.40314 1.57698 1.80259 0.90812 2.26324 1.14835 2.96786 1.63088 2.32643 3.01294
## Bacteroides_vulgatus 2.96186 2.72145 3.14976 2.63946 2.48610 1.13907 3.31856 3.57799 3.09254 2.91354 2.74777
## Bifidobacterium_adolescentis 5.61210 8.56589 4.65487 10.81433 7.48894 6.53874 3.67914 5.04893 4.97484 6.27492 7.89443
## Bacteroides_thetaiotaomicron 3.08880 2.69349 3.16444 2.91993 2.85340 2.73612 3.35522 3.27933 3.31300 2.86402 2.80401
## Streptococcus_salivarius 2.77444 3.02809 3.36832 2.02332 1.53413 3.34476 2.87564 3.03138 3.04584 3.40593 3.34746
## Dorea_formicigenerans 3.87336 5.77030 4.74969 3.53538 2.11433 5.06140 4.15264 4.08469 3.82179 4.98571 5.45250
## Bifidobacterium_pseudocatenulatum 6.94208 7.37838 6.99361 7.25508 7.47245 6.23862 7.24651 4.26102 5.33878 5.24604 5.91290
## Bacteroides_uniformis 2.04324 1.78350 2.02260 2.01742 1.98683 1.82686 2.04989 2.41251 2.38475 2.14047 1.77245
## Bacteroides_xylanisolvens 2.89389 1.56784 1.85183 2.81483 2.68261 1.41685 2.07120 2.13182 1.70626 1.60105 2.74080
## Prevotella_copri 1.78612 1.79223 1.83212 1.42012 1.17209 2.40416 1.65334 1.96898 1.69163 1.79573 1.88316
## Faecalibacterium_prausnitzii 0.64940 0.70535 0.60128 0.56506 0.64019 0.88437 0.50048 0.45379 0.61515 0.73538 0.55683
## Collinsella_aerofaciens 0.70488 0.63986 0.58174 0.67414 0.83075 0.76540 0.52348 0.42563 0.65863 0.58767 0.54864
## Lachnospiraceae_bacterium_5_1_63FAA 0.08142 0.27602 0.12902 0.14446 0.04769 0.15494 0.08348 0.13126 0.07500 0.16364 0.28232
## Roseburia_hominis 0.04609 0.04508 0.04129 0.03465 0.04144 0.05359 0.03803 0.05785 0.04990 0.04607 0.05414
## 16048 16316 16319 16347 16379 16416 16643 17346 17358 17367 17447
## Bifidobacterium_longum 9.69043 7.52306 7.55665 9.70590 6.84815 9.89749 11.31632 7.66734 9.86840 10.87283 3.25866
## Bacteroides_ovatus 3.03531 3.32437 3.45295 3.62218 3.75943 2.96599 3.02706 3.40560 3.41400 3.08738 6.09596
## Coprococcus_comes 2.96924 3.59466 3.57862 1.76048 2.61452 2.04108 1.76011 3.69207 2.09069 2.24782 2.02841
## Bacteroides_vulgatus 3.09935 3.44793 3.53090 3.23231 3.49744 2.82052 3.00506 3.46903 3.43126 3.08539 6.05372
## Bifidobacterium_adolescentis 6.52876 5.88728 5.87504 4.35779 4.40074 5.76228 5.49289 6.01398 5.36079 6.43311 2.12800
## Bacteroides_thetaiotaomicron 3.13347 3.04083 3.11459 3.14863 3.26102 3.08699 3.02583 3.08416 3.41487 3.08820 5.93408
## Streptococcus_salivarius 3.71090 3.67183 3.79982 3.06091 3.75770 3.55959 3.12754 3.69879 3.50295 3.44364 1.88983
## Dorea_formicigenerans 4.72522 4.64591 4.55858 2.69263 3.56759 4.79519 4.50406 4.68564 4.01979 4.17924 1.81824
## Bifidobacterium_pseudocatenulatum 5.77564 4.57475 4.62962 4.96492 3.94615 6.14754 7.24626 4.57054 6.23848 6.40033 2.29354
## Bacteroides_uniformis 1.98889 2.21392 2.01888 2.42394 2.38767 2.05014 2.07140 2.26052 2.19181 2.14782 3.36615
## Bacteroides_xylanisolvens 1.62204 3.19530 2.09612 3.13471 3.43980 1.53912 1.63411 1.87350 3.22991 2.79352 4.25302
## Prevotella_copri 2.07287 1.97112 1.93353 1.71181 1.91259 1.90389 1.82113 1.97873 2.03877 1.98940 3.87635
## Faecalibacterium_prausnitzii 0.90999 0.47017 0.44729 0.57450 0.52308 0.68340 0.62311 0.47828 0.71111 0.83658 0.71278
## Collinsella_aerofaciens 0.67753 0.37548 0.39634 0.58473 0.44993 0.63777 0.67223 0.42236 0.62913 0.68843 0.11636
## Lachnospiraceae_bacterium_5_1_63FAA 0.20016 0.21536 0.24479 0.05832 0.10769 0.14313 0.10475 0.22438 0.11106 0.11605 0.10150
## Roseburia_hominis 0.05873 0.03554 0.03999 0.04928 0.04970 0.04974 0.04541 0.05218 0.06504 0.05955 0.07687
## 17574 17614 17907 18003 18123 18158 18254 18652 18748 18883 19025
## Bifidobacterium_longum 9.70406 12.12046 11.29858 12.01189 12.41898 4.70889 9.50685 8.61060 10.72595 2.23603 11.74855
## Bacteroides_ovatus 3.54582 3.36962 3.43196 3.25432 3.33751 4.70126 3.99162 3.65097 3.61472 4.00635 3.48854
## Coprococcus_comes 2.65329 1.61138 1.25244 1.16593 1.32943 1.40043 1.30588 2.02912 1.43181 1.89141 1.34869
## Bacteroides_vulgatus 3.56764 3.17270 3.06646 2.90266 2.94911 4.49320 3.65775 1.26550 3.17810 4.38594 3.23491
## Bifidobacterium_adolescentis 6.20718 5.07402 4.43160 4.60358 4.28572 1.30207 2.33770 3.42930 4.09908 0.94154 3.49924
## Bacteroides_thetaiotaomicron 3.56745 3.27350 3.26772 3.23674 3.41009 4.11730 3.64058 3.49090 3.39957 3.64130 3.39626
## Streptococcus_salivarius 2.80874 3.07036 2.35949 2.37727 2.65054 2.85711 2.75597 3.69704 2.82017 3.50685 2.92942
## Dorea_formicigenerans 5.04111 3.41703 2.39040 2.56918 2.72636 2.71430 2.65012 3.86167 2.61596 3.73633 3.41932
## Bifidobacterium_pseudocatenulatum 7.95284 7.22140 5.17439 6.28844 3.52229 3.57447 5.32369 4.92522 5.16928 1.98442 6.81628
## Bacteroides_uniformis 2.19323 2.31014 2.40477 2.34879 2.39751 2.37414 2.45354 2.46187 2.60847 1.67152 2.32171
## Bacteroides_xylanisolvens 3.45689 1.71452 3.01134 2.84196 3.26709 3.28925 2.01041 3.45202 1.59493 4.40960 1.76766
## Prevotella_copri 2.16416 1.90331 1.42260 1.55162 1.66520 1.44533 1.65372 2.31028 1.58613 1.18808 1.70884
## Faecalibacterium_prausnitzii 1.03155 0.66410 0.55844 0.56703 0.73728 0.25535 0.43809 0.69166 0.55123 0.15787 0.62797
## Collinsella_aerofaciens 0.66214 0.71605 0.62589 0.62440 0.82628 0.23027 0.48497 0.44362 0.56426 0.10648 0.66458
## Lachnospiraceae_bacterium_5_1_63FAA 0.14738 0.07041 0.04965 0.03878 0.06610 0.05536 0.05088 0.07484 0.05303 0.13114 0.05452
## Roseburia_hominis 0.06064 0.05456 0.03377 0.04043 0.05243 0.02538 0.04090 0.04658 0.03987 0.02035 0.03542
## 19151 19175 7682 7683 7684 7685 7842 7843 7844 7845 8108
## Bifidobacterium_longum 12.83975 9.35652 10.61692 9.70452 10.26646 7.90970 11.09287 11.49847 12.31085 11.76466 9.55827
## Bacteroides_ovatus 3.42018 3.75385 3.09351 3.31482 3.12081 3.31232 3.53564 3.46157 3.38687 3.44778 3.66184
## Coprococcus_comes 1.07983 1.49248 2.25102 2.31762 2.12264 2.45777 1.21536 1.14849 1.07774 1.08142 1.32528
## Bacteroides_vulgatus 3.14217 3.41299 3.05040 3.30423 3.22814 3.27619 3.28027 3.18516 3.11734 3.07863 3.52520
## Bifidobacterium_adolescentis 3.48965 3.62408 7.16903 6.45453 6.70040 6.27837 4.72418 4.74670 4.96916 4.86254 4.15176
## Bacteroides_thetaiotaomicron 3.24309 3.31257 3.27164 3.33818 3.30218 3.46399 3.39208 3.37336 3.33352 3.35704 3.39183
## Streptococcus_salivarius 2.45071 3.03755 3.05755 3.16055 3.01270 3.87922 2.89674 2.66865 2.60725 2.59000 3.08853
## Dorea_formicigenerans 2.69458 3.28704 4.86800 5.05830 5.04009 5.51199 3.42631 3.08640 3.15582 2.74630 3.58930
## Bifidobacterium_pseudocatenulatum 7.13176 5.15000 6.09864 6.02910 6.40770 5.17550 5.83949 5.98674 7.11737 5.97672 5.82470
## Bacteroides_uniformis 2.30261 2.36019 2.27961 2.24583 1.91842 2.19582 2.40040 2.31289 2.33899 2.40465 2.29439
## Bacteroides_xylanisolvens 1.74067 3.38269 3.18674 3.28090 3.16414 3.41045 1.74224 3.26467 1.68023 1.61949 3.44844
## Prevotella_copri 1.59313 1.67610 1.83093 1.78060 1.72074 2.06993 1.59277 1.59619 1.60078 1.62372 1.66857
## Faecalibacterium_prausnitzii 0.57442 0.47734 0.48718 0.44086 0.46882 0.50270 0.53280 0.54786 0.57838 0.53260 0.49590
## Collinsella_aerofaciens 0.70420 0.49820 0.46253 0.41782 0.49708 0.44309 0.65567 0.67716 0.74469 0.66016 0.56383
## Lachnospiraceae_bacterium_5_1_63FAA 0.03893 0.06620 0.21907 0.24488 0.24101 0.28909 0.06532 0.06853 0.05540 0.05118 0.09357
## Roseburia_hominis 0.04302 0.03460 0.04239 0.03360 0.03617 0.02561 0.04120 0.03532 0.03681 0.03786 0.03727
## 8635 8952 9456 9474 refE mean
## Bifidobacterium_longum 11.16770 4.86230 6.59407 10.18399 0.01646 9.56031933
## Bacteroides_ovatus 3.98663 4.11944 3.92516 2.55709 0.25782 3.38335083
## Coprococcus_comes 1.15150 1.33169 1.19713 2.89442 0.01444 2.05775917
## Bacteroides_vulgatus 3.62765 4.19069 3.80546 2.61231 2.14684 3.19229017
## Bifidobacterium_adolescentis 2.92750 1.96201 2.61821 9.42034 0.04649 5.16690850
## Bacteroides_thetaiotaomicron 3.96140 4.19124 3.99868 2.51572 1.47422 3.26234733
## Streptococcus_salivarius 2.21486 3.35305 3.19640 4.85477 0.02846 3.03073567
## Dorea_formicigenerans 2.38047 3.72882 3.78772 9.53378 0.02775 3.90007033
## Bifidobacterium_pseudocatenulatum 4.42916 3.93062 5.15710 6.29975 0.15023 5.47845067
## Bacteroides_uniformis 2.53793 2.12691 2.16248 1.81519 0.21061 2.18617133
## Bacteroides_xylanisolvens 2.09226 4.32609 3.18280 2.51190 0.32466 2.55669967
## Prevotella_copri 1.40278 1.52016 1.60503 2.15390 60.84109 2.80426200
## Faecalibacterium_prausnitzii 0.56323 0.26951 0.39457 0.83952 1.61939 0.61356583
## Collinsella_aerofaciens 0.69060 0.26595 0.35697 0.66164 0.07251 0.55337850
## Lachnospiraceae_bacterium_5_1_63FAA 0.05638 0.12398 0.09152 0.28340 0.06825 0.12271150
## Roseburia_hominis 0.04124 0.02332 0.02846 0.05067 0.01307 0.04446167
## Evaluation
## Bifidobacterium_longum refE didn't pass the threshold (2023-04-12 14:11:30).
## Bacteroides_ovatus refE didn't pass the threshold (2023-04-12 14:11:30).
## Coprococcus_comes refE didn't pass the threshold (2023-04-12 14:11:30).
## Bacteroides_vulgatus refE didn't pass the threshold (2023-04-12 14:11:30).
## Bifidobacterium_adolescentis refE didn't pass the threshold (2023-04-12 14:11:30).
## Bacteroides_thetaiotaomicron refE didn't pass the threshold (2023-04-12 14:11:30).
## Streptococcus_salivarius refE didn't pass the threshold (2023-04-12 14:11:30).
## Dorea_formicigenerans refE didn't pass the threshold (2023-04-12 14:11:30).
## Bifidobacterium_pseudocatenulatum refE didn't pass the threshold (2023-04-12 14:11:30).
## Bacteroides_uniformis refE didn't pass the threshold (2023-04-12 14:11:30).
## Bacteroides_xylanisolvens refE didn't pass the threshold (2023-04-12 14:11:30).
## Prevotella_copri refE didn't pass the threshold (2023-04-12 14:11:30).
## Faecalibacterium_prausnitzii refE didn't pass the threshold (2023-04-12 14:11:30).
## Collinsella_aerofaciens refE didn't pass the threshold (2023-04-12 14:11:30).
## Lachnospiraceae_bacterium_5_1_63FAA refE didn't pass the threshold (2023-04-12 14:11:30).
## Roseburia_hominis refE didn't pass the threshold (2023-04-12 14:11:30).
## [ reached 'max' / getOption("max.print") -- omitted 1 rows ]3.2 Spike-in sample’s (BRS) remove
metaphlan2_ps_LOD_species_remove_BRS <- get_GroupPhyloseq(
ps = metaphlan2_ps_LOD_species,
group = "Group",
group_names = "QC",
discard = TRUE)
metaphlan2_ps_LOD_species_remove_BRS## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 192 taxa and 22 samples ]
## sample_data() Sample Data: [ 22 samples by 2 sample variables ]
## tax_table() Taxonomy Table: [ 192 taxa by 7 taxonomic ranks ]3.3 Systematic Information
devtools::session_info()## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.2 (2021-11-01)
## os macOS Monterey 12.2.1
## system x86_64, darwin17.0
## ui RStudio
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Asia/Shanghai
## date 2023-04-12
## rstudio 2022.07.2+576 Spotted Wakerobin (desktop)
## pandoc 2.19.2 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## abind 1.4-5 2016-07-21 [1] CRAN (R 4.1.0)
## ade4 1.7-18 2021-09-16 [1] CRAN (R 4.1.0)
## annotate 1.72.0 2021-10-26 [1] Bioconductor
## AnnotationDbi 1.60.2 2023-03-10 [1] Bioconductor
## ape 5.6-2 2022-03-02 [1] CRAN (R 4.1.2)
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0)
## backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.0)
## base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.1.0)
## Biobase 2.54.0 2021-10-26 [1] Bioconductor
## BiocGenerics 0.40.0 2021-10-26 [1] Bioconductor
## BiocParallel 1.28.3 2021-12-09 [1] Bioconductor
## biomformat 1.22.0 2021-10-26 [1] Bioconductor
## Biostrings 2.62.0 2021-10-26 [1] Bioconductor
## bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.0)
## bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.0)
## bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.0)
## blob 1.2.2 2021-07-23 [1] CRAN (R 4.1.0)
## bookdown 0.29 2022-09-12 [1] CRAN (R 4.1.2)
## brio 1.1.3 2021-11-30 [1] CRAN (R 4.1.0)
## broom 1.0.1 2022-08-29 [1] CRAN (R 4.1.2)
## bslib 0.4.0 2022-07-16 [1] CRAN (R 4.1.2)
## cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.0)
## callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0)
## car 3.0-12 2021-11-06 [1] CRAN (R 4.1.0)
## carData 3.0-5 2022-01-06 [1] CRAN (R 4.1.2)
## caTools 1.18.2 2021-03-28 [1] CRAN (R 4.1.0)
## cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.1.0)
## checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.0)
## cli 3.4.1 2022-09-23 [1] CRAN (R 4.1.2)
## cluster 2.1.2 2021-04-17 [1] CRAN (R 4.1.2)
## codetools 0.2-18 2020-11-04 [1] CRAN (R 4.1.2)
## coin 1.4-2 2021-10-08 [1] CRAN (R 4.1.0)
## colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.1.2)
## corpcor 1.6.10 2021-09-16 [1] CRAN (R 4.1.0)
## cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.1.0)
## crayon 1.5.0 2022-02-14 [1] CRAN (R 4.1.2)
## crosstalk 1.2.0 2021-11-04 [1] CRAN (R 4.1.0)
## data.table 1.14.6 2022-11-16 [1] CRAN (R 4.1.2)
## DBI 1.1.2 2021-12-20 [1] CRAN (R 4.1.0)
## DelayedArray 0.20.0 2021-10-26 [1] Bioconductor
## desc 1.4.1 2022-03-06 [1] CRAN (R 4.1.2)
## DESeq2 1.34.0 2021-10-26 [1] Bioconductor
## devtools 2.4.3 2021-11-30 [1] CRAN (R 4.1.0)
## digest 0.6.30 2022-10-18 [1] CRAN (R 4.1.2)
## doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.1.2)
## doSNOW 1.0.20 2022-02-04 [1] CRAN (R 4.1.2)
## dplyr * 1.0.10 2022-09-01 [1] CRAN (R 4.1.2)
## DT 0.21 2022-02-26 [1] CRAN (R 4.1.2)
## dynamicTreeCut 1.63-1 2016-03-11 [1] CRAN (R 4.1.0)
## edgeR 3.36.0 2021-10-26 [1] Bioconductor
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
## evaluate 0.17 2022-10-07 [1] CRAN (R 4.1.2)
## fansi 1.0.2 2022-01-14 [1] CRAN (R 4.1.2)
## farver 2.1.0 2021-02-28 [1] CRAN (R 4.1.0)
## fastcluster 1.2.3 2021-05-24 [1] CRAN (R 4.1.0)
## fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0)
## fdrtool 1.2.17 2021-11-13 [1] CRAN (R 4.1.0)
## filematrix 1.3 2018-02-27 [1] CRAN (R 4.1.0)
## foreach 1.5.2 2022-02-02 [1] CRAN (R 4.1.2)
## foreign 0.8-82 2022-01-13 [1] CRAN (R 4.1.2)
## forestplot 2.0.1 2021-09-03 [1] CRAN (R 4.1.0)
## Formula 1.2-4 2020-10-16 [1] CRAN (R 4.1.0)
## fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.0)
## genefilter 1.76.0 2021-10-26 [1] Bioconductor
## geneplotter 1.72.0 2021-10-26 [1] Bioconductor
## generics 0.1.2 2022-01-31 [1] CRAN (R 4.1.2)
## GenomeInfoDb 1.30.1 2022-01-30 [1] Bioconductor
## GenomeInfoDbData 1.2.7 2022-03-09 [1] Bioconductor
## GenomicRanges 1.46.1 2021-11-18 [1] Bioconductor
## ggiraph 0.8.2 2022-02-22 [1] CRAN (R 4.1.2)
## ggiraphExtra 0.3.0 2020-10-06 [1] CRAN (R 4.1.2)
## ggplot2 * 3.4.0 2022-11-04 [1] CRAN (R 4.1.2)
## ggpubr * 0.4.0 2020-06-27 [1] CRAN (R 4.1.0)
## ggrepel 0.9.1 2021-01-15 [1] CRAN (R 4.1.0)
## ggsignif 0.6.3 2021-09-09 [1] CRAN (R 4.1.0)
## glasso 1.11 2019-10-01 [1] CRAN (R 4.1.0)
## glmnet 4.1-3 2021-11-02 [1] CRAN (R 4.1.0)
## glue * 1.6.2 2022-02-24 [1] CRAN (R 4.1.2)
## Gmisc * 3.0.0 2022-01-03 [1] CRAN (R 4.1.2)
## GO.db 3.14.0 2022-04-11 [1] Bioconductor
## gplots 3.1.1 2020-11-28 [1] CRAN (R 4.1.0)
## gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0)
## gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
## gtools 3.9.2 2021-06-06 [1] CRAN (R 4.1.0)
## highr 0.9 2021-04-16 [1] CRAN (R 4.1.0)
## Hmisc 4.6-0 2021-10-07 [1] CRAN (R 4.1.0)
## htmlTable * 2.4.0 2022-01-04 [1] CRAN (R 4.1.2)
## htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.1.2)
## htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.1.0)
## httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.0)
## huge 1.3.5 2021-06-30 [1] CRAN (R 4.1.0)
## igraph 1.2.11 2022-01-04 [1] CRAN (R 4.1.2)
## impute 1.68.0 2021-10-26 [1] Bioconductor
## insight 0.17.0 2022-03-29 [1] CRAN (R 4.1.2)
## IRanges 2.28.0 2021-10-26 [1] Bioconductor
## irlba 2.3.5 2021-12-06 [1] CRAN (R 4.1.0)
## iterators 1.0.14 2022-02-05 [1] CRAN (R 4.1.2)
## jpeg 0.1-9 2021-07-24 [1] CRAN (R 4.1.0)
## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.1.0)
## jsonlite 1.8.3 2022-10-21 [1] CRAN (R 4.1.2)
## KEGGREST 1.34.0 2021-10-26 [1] Bioconductor
## KernSmooth 2.23-20 2021-05-03 [1] CRAN (R 4.1.2)
## knitr 1.40 2022-08-24 [1] CRAN (R 4.1.2)
## labeling 0.4.2 2020-10-20 [1] CRAN (R 4.1.0)
## lattice 0.20-45 2021-09-22 [1] CRAN (R 4.1.2)
## latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.1.0)
## lavaan 0.6-11 2022-03-31 [1] CRAN (R 4.1.2)
## libcoin 1.0-9 2021-09-27 [1] CRAN (R 4.1.0)
## lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.1.2)
## limma 3.50.1 2022-02-17 [1] Bioconductor
## locfit 1.5-9.5 2022-03-03 [1] CRAN (R 4.1.2)
## lubridate 1.8.0 2021-10-07 [1] CRAN (R 4.1.0)
## magrittr * 2.0.3 2022-03-30 [1] CRAN (R 4.1.2)
## MASS 7.3-55 2022-01-13 [1] CRAN (R 4.1.2)
## Matrix 1.4-0 2021-12-08 [1] CRAN (R 4.1.0)
## MatrixGenerics 1.6.0 2021-10-26 [1] Bioconductor
## matrixStats 0.61.0 2021-09-17 [1] CRAN (R 4.1.0)
## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.0)
## metagenomeSeq 1.36.0 2021-10-26 [1] Bioconductor
## mgcv 1.8-39 2022-02-24 [1] CRAN (R 4.1.2)
## mixedCCA 1.5.2 2022-07-14 [1] Github (irinagain/mixedCCA@c6d41a3)
## mnormt 2.0.2 2020-09-01 [1] CRAN (R 4.1.0)
## modeltools 0.2-23 2020-03-05 [1] CRAN (R 4.1.0)
## multcomp 1.4-18 2022-01-04 [1] CRAN (R 4.1.2)
## multtest 2.50.0 2021-10-26 [1] Bioconductor
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
## mvtnorm 1.1-3 2021-10-08 [1] CRAN (R 4.1.0)
## mycor 0.1.1 2018-04-10 [1] CRAN (R 4.1.0)
## NetCoMi 1.0.3 2022-07-14 [1] Github (stefpeschel/NetCoMi@d4d80d3)
## nlme 3.1-155 2022-01-13 [1] CRAN (R 4.1.2)
## nnet 7.3-17 2022-01-13 [1] CRAN (R 4.1.2)
## pbapply 1.5-0 2021-09-16 [1] CRAN (R 4.1.0)
## pbivnorm 0.6.0 2015-01-23 [1] CRAN (R 4.1.0)
## pcaPP 1.9-74 2021-04-23 [1] CRAN (R 4.1.0)
## permute 0.9-7 2022-01-27 [1] CRAN (R 4.1.2)
## pheatmap 1.0.12 2019-01-04 [1] CRAN (R 4.1.0)
## phyloseq * 1.38.0 2021-10-26 [1] Bioconductor
## pillar 1.7.0 2022-02-01 [1] CRAN (R 4.1.2)
## pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.1.0)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
## pkgload 1.2.4 2021-11-30 [1] CRAN (R 4.1.0)
## plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0)
## png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0)
## ppcor 1.1 2015-12-03 [1] CRAN (R 4.1.0)
## preprocessCore 1.56.0 2021-10-26 [1] Bioconductor
## prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
## processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.0)
## ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.0)
## psych 2.2.5 2022-05-10 [1] CRAN (R 4.1.2)
## pulsar 0.3.7 2020-08-07 [1] CRAN (R 4.1.0)
## purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
## qgraph 1.9.2 2022-03-04 [1] CRAN (R 4.1.2)
## R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0)
## rbibutils 2.2.7 2021-12-07 [1] CRAN (R 4.1.0)
## RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0)
## Rcpp * 1.0.10 2023-01-22 [1] CRAN (R 4.1.2)
## RCurl 1.98-1.6 2022-02-08 [1] CRAN (R 4.1.2)
## Rdpack 2.2 2022-03-19 [1] CRAN (R 4.1.2)
## readxl 1.4.0 2022-03-28 [1] CRAN (R 4.1.2)
## remotes 2.4.2 2021-11-30 [1] CRAN (R 4.1.0)
## reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.1.0)
## rhdf5 2.38.1 2022-03-10 [1] Bioconductor
## rhdf5filters 1.6.0 2021-10-26 [1] Bioconductor
## Rhdf5lib 1.16.0 2021-10-26 [1] Bioconductor
## rlang 1.0.6 2022-09-24 [1] CRAN (R 4.1.2)
## rmarkdown 2.17 2022-10-07 [1] CRAN (R 4.1.2)
## rootSolve 1.8.2.3 2021-09-29 [1] CRAN (R 4.1.0)
## rpart 4.1.16 2022-01-24 [1] CRAN (R 4.1.2)
## rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.0)
## RSQLite 2.2.10 2022-02-17 [1] CRAN (R 4.1.2)
## rstatix 0.7.0 2021-02-13 [1] CRAN (R 4.1.0)
## rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
## S4Vectors 0.32.3 2021-11-21 [1] Bioconductor
## sandwich 3.0-1 2021-05-18 [1] CRAN (R 4.1.0)
## sass 0.4.2 2022-07-16 [1] CRAN (R 4.1.2)
## scales 1.2.1 2022-08-20 [1] CRAN (R 4.1.2)
## sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.0)
## shape 1.4.6 2021-05-19 [1] CRAN (R 4.1.0)
## sjlabelled 1.2.0 2022-04-10 [1] CRAN (R 4.1.2)
## sjmisc 2.8.9 2021-12-03 [1] CRAN (R 4.1.0)
## snow 0.4-4 2021-10-27 [1] CRAN (R 4.1.0)
## SpiecEasi 1.1.2 2022-07-14 [1] Github (zdk123/SpiecEasi@c463727)
## SPRING 1.0.4 2022-08-03 [1] Github (GraceYoon/SPRING@3d641a4)
## stringi 1.7.8 2022-07-11 [1] CRAN (R 4.1.2)
## stringr 1.4.1 2022-08-20 [1] CRAN (R 4.1.2)
## SummarizedExperiment 1.24.0 2021-10-26 [1] Bioconductor
## survival 3.4-0 2022-08-09 [1] CRAN (R 4.1.2)
## systemfonts 1.0.4 2022-02-11 [1] CRAN (R 4.1.2)
## testthat 3.1.2 2022-01-20 [1] CRAN (R 4.1.2)
## TH.data 1.1-0 2021-09-27 [1] CRAN (R 4.1.0)
## tibble * 3.1.8 2022-07-22 [1] CRAN (R 4.1.2)
## tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.1.2)
## tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.1.2)
## tmvnsim 1.0-2 2016-12-15 [1] CRAN (R 4.1.0)
## usethis 2.1.5 2021-12-09 [1] CRAN (R 4.1.0)
## utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0)
## uuid 1.0-3 2021-11-01 [1] CRAN (R 4.1.0)
## vctrs 0.5.1 2022-11-16 [1] CRAN (R 4.1.2)
## vegan 2.5-7 2020-11-28 [1] CRAN (R 4.1.0)
## VGAM 1.1-6 2022-02-14 [1] CRAN (R 4.1.2)
## WGCNA 1.71 2022-04-22 [1] CRAN (R 4.1.2)
## withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.2)
## Wrench 1.12.0 2021-10-26 [1] Bioconductor
## xfun 0.34 2022-10-18 [1] CRAN (R 4.1.2)
## XMAS2 * 2.1.8.7 2023-01-06 [1] local
## XML 3.99-0.9 2022-02-24 [1] CRAN (R 4.1.2)
## xtable 1.8-4 2019-04-21 [1] CRAN (R 4.1.0)
## XVector 0.34.0 2021-10-26 [1] Bioconductor
## yaml 2.3.6 2022-10-18 [1] CRAN (R 4.1.2)
## zlibbioc 1.40.0 2021-10-26 [1] Bioconductor
## zoo 1.8-9 2021-03-09 [1] CRAN (R 4.1.0)
##
## [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
##
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────