Chapter 3 Quality Control
Loading packages
Quality control of DADA2 results will help us have more rational determinations on the further data analysis.
3.1 Reads’ track by DADA2
Figure 3.1: Reads’ track by DADA2
The percentage of the final remained read counts approximate 70%, indicating that we should consider the sequence depth for analysis when we build the sequence library.
3.2 Spike-in sample (BRS) assessment
The taxonomic levels of spike-in sample’s bacteria is genus. Firstly, using the summarize_taxa to get the genus level phyloseq object and get the BRS_ID.
## Group
## S6030 BB
## S6032 BB
## S6033 BB
## S6035 AA
## S6036 BB
## S6037 AA
## S6040 BB
## S6043 AA
## S6045 BB
## S6046 BB
## S6048 BB
## S6049 AA
## S6050 BB
## S6054 BB
## S6055 BB
## S6058 BB
## S6059 AA
## S6060 AA
## S6061 AA
## S6063 BB
## S6065 AA
## S6066 AA
## S6068 BB
## S8005 QCdo run_RefCheck2 under the optimal parameters.
BRS_ID: the ID of BRS sample;
Reference: the directory of the latest spike-in sample matrix (default: /share/projects/Analytics/analytics/XMAS/RefCheck/);
Save: the directory to save the latest spike-in sample matrix (default: /share/projects/Analytics/analytics/XMAS/RefCheck/).
To see more details to use ?run_RefCheck2.
## Noting: the Reference Matrix is for 16s
## S8005 is in the Reference Matrix's samples and remove it to run
##
## ############Matched baterica of the BRS sample#############
## The number of BRS' bacteria matched the Reference Matrix is [15]
## g__Bifidobacterium
## g__Bacteroides
## g__Faecalibacterium
## g__Lactobacillus
## g__Parabacteroides
## g__Collinsella
## g__Coprococcus_3
## g__Dorea
## g__Streptococcus
## g__Roseburia
## g__Anaerostipes
## g__Escherichia_Shigella
## g__Enterococcus
## g__Prevotella_9
## g__Eggerthella
##
## The number of the additional bacteria compared to Reference Matrix is [1]
## ###########################################################
##
## ##################Status of the BRS sample##################
## Whether the BRS has the all bateria of Reference Matrix: TRUE
## Correlation Coefficient of the BRS is: 0.9714
## Bray Curtis of the BRS is: 0.07607
## Impurity of Max additional genus (g__Cutibacterium) of the BRS is: 0.06409
## ###########################################################
## #####Final Evaluation Results of the BRS #######
## The BRS of sequencing dataset passed the cutoff of the Reference Matrix
## Cutoff of Coefficient is 0.8946
## Cutoff of BrayCurtis is 0.1425
## Cutoff of Impurity is 0.1565
## ###########################################################
## Gold_Cutoff BRS
## Coef 0.8946 0.97140
## Bray 0.1425 0.07607
## Impurity(max) 1.0000 0.064093.3 Spike-in sample’s (BRS) remove
After evaluating the sequencing quality, we remove the BRS.
dada2_ps_remove_BRS <- get_GroupPhyloseq(
ps = dada2_ps,
group = "Group",
group_names = "QC",
discard = TRUE)
dada2_ps_remove_BRS## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 896 taxa and 23 samples ]
## sample_data() Sample Data: [ 23 samples by 1 sample variables ]
## tax_table() Taxonomy Table: [ 896 taxa by 7 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 896 tips and 893 internal nodes ]
## refseq() DNAStringSet: [ 896 reference sequences ]3.4 Rarefaction curves
plot_RarefCurve(ps = dada2_ps_remove_BRS,
taxa_level = "OTU",
step = 100,
label = "Group",
color = "Group")## rarefying sample S6030
## rarefying sample S6032
## rarefying sample S6033
## rarefying sample S6035
## rarefying sample S6036
## rarefying sample S6037
## rarefying sample S6040
## rarefying sample S6043
## rarefying sample S6045
## rarefying sample S6046
## rarefying sample S6048
## rarefying sample S6049
## rarefying sample S6050
## rarefying sample S6054
## rarefying sample S6055
## rarefying sample S6058
## rarefying sample S6059
## rarefying sample S6060
## rarefying sample S6061
## rarefying sample S6063
## rarefying sample S6065
## rarefying sample S6066
## rarefying sample S6068
Figure 3.2: Rarefaction curves
The result showed that all the samples had different sequence depth but had the full sample richness.
3.5 Summarize phyloseq-class object
Summarizing the phyloseq-class object by using summarize_phyloseq. It displayed that briefly introduction of the object.
summarize_phyloseq(ps = dada2_ps_remove_BRS)
## Compositional = NO2
## 1] Min. number of reads = 511812] Max. number of reads = 716673] Total number of reads = 14089154] Average number of reads = 61257.17391304355] Median number of reads = 614357] Sparsity = 0.8610248447204976] Any OTU sum to 1 or less? YES8] Number of singletons = 49] Percent of OTUs that are singletons
## (i.e. exactly one read detected across all samples)010] Number of sample variables are: 1Group2
## [[1]]
## [1] "1] Min. number of reads = 51181"
##
## [[2]]
## [1] "2] Max. number of reads = 71667"
##
## [[3]]
## [1] "3] Total number of reads = 1408915"
##
## [[4]]
## [1] "4] Average number of reads = 61257.1739130435"
##
## [[5]]
## [1] "5] Median number of reads = 61435"
##
## [[6]]
## [1] "7] Sparsity = 0.861024844720497"
##
## [[7]]
## [1] "6] Any OTU sum to 1 or less? YES"
##
## [[8]]
## [1] "8] Number of singletons = 4"
##
## [[9]]
## [1] "9] Percent of OTUs that are singletons\n (i.e. exactly one read detected across all samples)0"
##
## [[10]]
## [1] "10] Number of sample variables are: 1"
##
## [[11]]
## [1] "Group"The minus account of the OTU counts is 51181 in the phyloseq object, and we can use it as the threshold to rarefy.
Notice the Sparsity (0.86), indicating the data has many zeros and pay attention to the downstream data analysis. A common property of amplicon based microbiota data generated by sequencing.
3.6 Systematic Information
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.3 (2022-03-10)
## 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 2023-10-27
## rstudio 2023.09.0+463 Desert Sunflower (desktop)
## pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## abind 1.4-5 2016-07-21 [2] CRAN (R 4.1.0)
## ade4 1.7-22 2023-02-06 [2] CRAN (R 4.1.2)
## ALDEx2 1.30.0 2022-11-01 [2] Bioconductor
## annotate 1.72.0 2021-10-26 [2] Bioconductor
## AnnotationDbi 1.60.2 2023-03-10 [2] Bioconductor
## ape * 5.7-1 2023-03-13 [2] CRAN (R 4.1.2)
## askpass 1.1 2019-01-13 [2] CRAN (R 4.1.0)
## backports 1.4.1 2021-12-13 [2] CRAN (R 4.1.0)
## base64enc 0.1-3 2015-07-28 [2] CRAN (R 4.1.0)
## bayesm 3.1-5 2022-12-02 [2] CRAN (R 4.1.2)
## Biobase * 2.54.0 2021-10-26 [2] Bioconductor
## BiocGenerics * 0.40.0 2021-10-26 [2] Bioconductor
## BiocParallel 1.28.3 2021-12-09 [2] Bioconductor
## biomformat 1.22.0 2021-10-26 [2] Bioconductor
## Biostrings 2.62.0 2021-10-26 [2] Bioconductor
## bit 4.0.5 2022-11-15 [2] CRAN (R 4.1.2)
## bit64 4.0.5 2020-08-30 [2] CRAN (R 4.1.0)
## bitops 1.0-7 2021-04-24 [2] CRAN (R 4.1.0)
## blob 1.2.4 2023-03-17 [2] CRAN (R 4.1.2)
## bookdown 0.34 2023-05-09 [2] CRAN (R 4.1.2)
## broom 1.0.5 2023-06-09 [2] CRAN (R 4.1.3)
## bslib 0.5.0 2023-06-09 [2] CRAN (R 4.1.3)
## cachem 1.0.8 2023-05-01 [2] CRAN (R 4.1.2)
## callr 3.7.3 2022-11-02 [2] CRAN (R 4.1.2)
## car 3.1-2 2023-03-30 [2] CRAN (R 4.1.2)
## carData 3.0-5 2022-01-06 [2] CRAN (R 4.1.2)
## caTools 1.18.2 2021-03-28 [2] CRAN (R 4.1.0)
## cccd 1.6 2022-04-08 [2] CRAN (R 4.1.2)
## cellranger 1.1.0 2016-07-27 [2] CRAN (R 4.1.0)
## checkmate 2.2.0 2023-04-27 [2] CRAN (R 4.1.2)
## class 7.3-22 2023-05-03 [2] CRAN (R 4.1.2)
## classInt 0.4-9 2023-02-28 [2] CRAN (R 4.1.2)
## cli 3.6.1 2023-03-23 [2] CRAN (R 4.1.2)
## cluster 2.1.4 2022-08-22 [2] CRAN (R 4.1.2)
## coda 0.19-4 2020-09-30 [2] CRAN (R 4.1.0)
## codetools 0.2-19 2023-02-01 [2] CRAN (R 4.1.2)
## coin 1.4-2 2021-10-08 [2] CRAN (R 4.1.0)
## colorspace 2.1-0 2023-01-23 [2] CRAN (R 4.1.2)
## compositions 2.0-6 2023-04-13 [2] CRAN (R 4.1.2)
## conflicted * 1.2.0 2023-02-01 [2] CRAN (R 4.1.2)
## corpcor 1.6.10 2021-09-16 [2] CRAN (R 4.1.0)
## corrplot 0.92 2021-11-18 [2] CRAN (R 4.1.0)
## cowplot 1.1.1 2020-12-30 [2] CRAN (R 4.1.0)
## crayon 1.5.2 2022-09-29 [2] CRAN (R 4.1.2)
## crosstalk 1.2.0 2021-11-04 [2] CRAN (R 4.1.0)
## data.table 1.14.8 2023-02-17 [2] CRAN (R 4.1.2)
## DBI 1.1.3 2022-06-18 [2] CRAN (R 4.1.2)
## DelayedArray 0.20.0 2021-10-26 [2] Bioconductor
## deldir 1.0-9 2023-05-17 [2] CRAN (R 4.1.3)
## DEoptimR 1.0-14 2023-06-09 [2] CRAN (R 4.1.3)
## DESeq2 1.34.0 2021-10-26 [2] Bioconductor
## devtools * 2.4.5 2022-10-11 [2] CRAN (R 4.1.2)
## digest 0.6.33 2023-07-07 [1] CRAN (R 4.1.3)
## doParallel 1.0.17 2022-02-07 [2] CRAN (R 4.1.2)
## doSNOW 1.0.20 2022-02-04 [2] CRAN (R 4.1.2)
## dplyr * 1.1.2 2023-04-20 [2] CRAN (R 4.1.2)
## DT 0.28 2023-05-18 [2] CRAN (R 4.1.3)
## dynamicTreeCut 1.63-1 2016-03-11 [2] CRAN (R 4.1.0)
## e1071 1.7-13 2023-02-01 [2] CRAN (R 4.1.2)
## edgeR 3.36.0 2021-10-26 [2] Bioconductor
## ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.1.0)
## emmeans 1.8.7 2023-06-23 [1] CRAN (R 4.1.3)
## estimability 1.4.1 2022-08-05 [2] CRAN (R 4.1.2)
## evaluate 0.21 2023-05-05 [2] CRAN (R 4.1.2)
## FactoMineR 2.8 2023-03-27 [2] CRAN (R 4.1.2)
## fansi 1.0.4 2023-01-22 [2] CRAN (R 4.1.2)
## farver 2.1.1 2022-07-06 [2] CRAN (R 4.1.2)
## fastcluster 1.2.3 2021-05-24 [2] CRAN (R 4.1.0)
## fastmap 1.1.1 2023-02-24 [2] CRAN (R 4.1.2)
## fdrtool 1.2.17 2021-11-13 [2] CRAN (R 4.1.0)
## filematrix 1.3 2018-02-27 [2] CRAN (R 4.1.0)
## flashClust 1.01-2 2012-08-21 [2] CRAN (R 4.1.0)
## FNN 1.1.3.2 2023-03-20 [2] CRAN (R 4.1.2)
## foreach 1.5.2 2022-02-02 [2] CRAN (R 4.1.2)
## foreign 0.8-84 2022-12-06 [2] CRAN (R 4.1.2)
## forestplot 3.1.1 2022-12-06 [2] CRAN (R 4.1.2)
## formatR 1.14 2023-01-17 [2] CRAN (R 4.1.2)
## Formula 1.2-5 2023-02-24 [2] CRAN (R 4.1.2)
## fs 1.6.2 2023-04-25 [2] CRAN (R 4.1.2)
## futile.logger * 1.4.3 2016-07-10 [2] CRAN (R 4.1.0)
## futile.options 1.0.1 2018-04-20 [2] CRAN (R 4.1.0)
## genefilter 1.76.0 2021-10-26 [2] Bioconductor
## geneplotter 1.72.0 2021-10-26 [2] Bioconductor
## generics 0.1.3 2022-07-05 [2] CRAN (R 4.1.2)
## GenomeInfoDb * 1.30.1 2022-01-30 [2] Bioconductor
## GenomeInfoDbData 1.2.7 2022-03-09 [2] Bioconductor
## GenomicRanges * 1.46.1 2021-11-18 [2] Bioconductor
## ggiraph 0.8.7 2023-03-17 [2] CRAN (R 4.1.2)
## ggiraphExtra 0.3.0 2020-10-06 [2] CRAN (R 4.1.2)
## ggplot2 * 3.4.2 2023-04-03 [2] CRAN (R 4.1.2)
## ggpubr * 0.6.0 2023-02-10 [2] CRAN (R 4.1.2)
## ggrepel 0.9.3 2023-02-03 [2] CRAN (R 4.1.2)
## ggsci 3.0.0 2023-03-08 [2] CRAN (R 4.1.2)
## ggsignif 0.6.4 2022-10-13 [2] CRAN (R 4.1.2)
## ggVennDiagram 1.2.2 2022-09-08 [2] CRAN (R 4.1.2)
## glasso 1.11 2019-10-01 [2] CRAN (R 4.1.0)
## glmnet 4.1-7 2023-03-23 [2] CRAN (R 4.1.2)
## glue * 1.6.2 2022-02-24 [2] CRAN (R 4.1.2)
## Gmisc * 3.0.2 2023-03-13 [2] CRAN (R 4.1.2)
## GO.db 3.14.0 2022-04-11 [2] Bioconductor
## gplots 3.1.3 2022-04-25 [2] CRAN (R 4.1.2)
## gridExtra 2.3 2017-09-09 [2] CRAN (R 4.1.0)
## gtable 0.3.3 2023-03-21 [2] CRAN (R 4.1.2)
## gtools 3.9.4 2022-11-27 [2] CRAN (R 4.1.2)
## highr 0.10 2022-12-22 [2] CRAN (R 4.1.2)
## Hmisc 5.1-0 2023-05-08 [2] CRAN (R 4.1.2)
## hms 1.1.3 2023-03-21 [2] CRAN (R 4.1.2)
## htmlTable * 2.4.1 2022-07-07 [2] CRAN (R 4.1.2)
## htmltools 0.5.5 2023-03-23 [2] CRAN (R 4.1.2)
## htmlwidgets 1.6.2 2023-03-17 [2] CRAN (R 4.1.2)
## httpuv 1.6.11 2023-05-11 [2] CRAN (R 4.1.3)
## httr 1.4.6 2023-05-08 [2] CRAN (R 4.1.2)
## huge 1.3.5 2021-06-30 [2] CRAN (R 4.1.0)
## igraph 1.5.0 2023-06-16 [1] CRAN (R 4.1.3)
## impute 1.68.0 2021-10-26 [2] Bioconductor
## insight 0.19.3 2023-06-29 [2] CRAN (R 4.1.3)
## IRanges * 2.28.0 2021-10-26 [2] Bioconductor
## irlba 2.3.5.1 2022-10-03 [2] CRAN (R 4.1.2)
## iterators 1.0.14 2022-02-05 [2] CRAN (R 4.1.2)
## jpeg 0.1-10 2022-11-29 [2] CRAN (R 4.1.2)
## jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.1.0)
## jsonlite 1.8.7 2023-06-29 [2] CRAN (R 4.1.3)
## kableExtra 1.3.4 2021-02-20 [2] CRAN (R 4.1.2)
## KEGGREST 1.34.0 2021-10-26 [2] Bioconductor
## KernSmooth 2.23-22 2023-07-10 [2] CRAN (R 4.1.3)
## knitr 1.43 2023-05-25 [2] CRAN (R 4.1.3)
## labeling 0.4.2 2020-10-20 [2] CRAN (R 4.1.0)
## lambda.r 1.2.4 2019-09-18 [2] CRAN (R 4.1.0)
## later 1.3.1 2023-05-02 [2] CRAN (R 4.1.2)
## lattice * 0.21-8 2023-04-05 [2] CRAN (R 4.1.2)
## lavaan 0.6-15 2023-03-14 [2] CRAN (R 4.1.2)
## leaps 3.1 2020-01-16 [2] CRAN (R 4.1.0)
## libcoin 1.0-9 2021-09-27 [2] CRAN (R 4.1.0)
## lifecycle 1.0.3 2022-10-07 [2] CRAN (R 4.1.2)
## limma 3.50.3 2022-04-07 [2] Bioconductor
## locfit 1.5-9.8 2023-06-11 [2] CRAN (R 4.1.3)
## LOCOM 1.1 2022-08-05 [2] Github (yijuanhu/LOCOM@c181e0f)
## lubridate 1.9.2 2023-02-10 [2] CRAN (R 4.1.2)
## magrittr * 2.0.3 2022-03-30 [2] CRAN (R 4.1.2)
## MASS 7.3-60 2023-05-04 [2] CRAN (R 4.1.2)
## Matrix 1.6-0 2023-07-08 [2] CRAN (R 4.1.3)
## MatrixGenerics * 1.6.0 2021-10-26 [2] Bioconductor
## matrixStats * 1.0.0 2023-06-02 [2] CRAN (R 4.1.3)
## mbzinb 0.2 2022-03-16 [2] local
## memoise 2.0.1 2021-11-26 [2] CRAN (R 4.1.0)
## metagenomeSeq 1.36.0 2021-10-26 [2] Bioconductor
## mgcv 1.8-42 2023-03-02 [2] CRAN (R 4.1.2)
## microbiome 1.16.0 2021-10-26 [2] Bioconductor
## mime 0.12 2021-09-28 [2] CRAN (R 4.1.0)
## miniUI 0.1.1.1 2018-05-18 [2] CRAN (R 4.1.0)
## mixedCCA 1.6.2 2022-09-09 [2] CRAN (R 4.1.2)
## mnormt 2.1.1 2022-09-26 [2] CRAN (R 4.1.2)
## modeltools 0.2-23 2020-03-05 [2] CRAN (R 4.1.0)
## multcomp 1.4-25 2023-06-20 [2] CRAN (R 4.1.3)
## multcompView 0.1-9 2023-04-09 [2] CRAN (R 4.1.2)
## multtest 2.50.0 2021-10-26 [2] Bioconductor
## munsell 0.5.0 2018-06-12 [2] CRAN (R 4.1.0)
## mvtnorm 1.2-2 2023-06-08 [2] CRAN (R 4.1.3)
## mycor 0.1.1 2018-04-10 [2] CRAN (R 4.1.0)
## NADA 1.6-1.1 2020-03-22 [2] CRAN (R 4.1.0)
## NetCoMi * 1.0.3 2022-07-14 [2] Github (stefpeschel/NetCoMi@d4d80d3)
## nlme * 3.1-162 2023-01-31 [2] CRAN (R 4.1.2)
## nnet 7.3-19 2023-05-03 [2] CRAN (R 4.1.2)
## openssl 2.0.6 2023-03-09 [2] CRAN (R 4.1.2)
## pbapply 1.7-2 2023-06-27 [2] CRAN (R 4.1.3)
## pbivnorm 0.6.0 2015-01-23 [2] CRAN (R 4.1.0)
## pcaPP 2.0-3 2022-10-24 [2] CRAN (R 4.1.2)
## permute * 0.9-7 2022-01-27 [2] CRAN (R 4.1.2)
## pheatmap * 1.0.12 2019-01-04 [2] CRAN (R 4.1.0)
## phyloseq * 1.38.0 2021-10-26 [2] Bioconductor
## picante * 1.8.2 2020-06-10 [2] CRAN (R 4.1.0)
## pillar 1.9.0 2023-03-22 [2] CRAN (R 4.1.2)
## pkgbuild 1.4.2 2023-06-26 [2] CRAN (R 4.1.3)
## pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.1.0)
## pkgload 1.3.2.1 2023-07-08 [2] CRAN (R 4.1.3)
## plyr 1.8.8 2022-11-11 [2] CRAN (R 4.1.2)
## png 0.1-8 2022-11-29 [2] CRAN (R 4.1.2)
## ppcor 1.1 2015-12-03 [2] CRAN (R 4.1.0)
## preprocessCore 1.56.0 2021-10-26 [2] Bioconductor
## prettyunits 1.1.1 2020-01-24 [2] CRAN (R 4.1.0)
## processx 3.8.2 2023-06-30 [2] CRAN (R 4.1.3)
## profvis 0.3.8 2023-05-02 [2] CRAN (R 4.1.2)
## promises 1.2.0.1 2021-02-11 [2] CRAN (R 4.1.0)
## protoclust 1.6.4 2022-04-01 [2] CRAN (R 4.1.2)
## proxy 0.4-27 2022-06-09 [2] CRAN (R 4.1.2)
## ps 1.7.5 2023-04-18 [2] CRAN (R 4.1.2)
## pscl 1.5.5.1 2023-05-10 [2] CRAN (R 4.1.2)
## psych 2.3.6 2023-06-21 [2] CRAN (R 4.1.3)
## pulsar 0.3.10 2023-01-26 [2] CRAN (R 4.1.2)
## purrr * 1.0.1 2023-01-10 [2] CRAN (R 4.1.2)
## qgraph 1.9.5 2023-05-16 [2] CRAN (R 4.1.3)
## quadprog 1.5-8 2019-11-20 [2] CRAN (R 4.1.0)
## qvalue 2.26.0 2021-10-26 [2] Bioconductor
## R6 2.5.1 2021-08-19 [2] CRAN (R 4.1.0)
## RAIDA 1.0 2022-03-14 [2] local
## rbibutils 2.2.13 2023-01-13 [2] CRAN (R 4.1.2)
## RColorBrewer * 1.1-3 2022-04-03 [2] CRAN (R 4.1.2)
## Rcpp * 1.0.11 2023-07-06 [1] CRAN (R 4.1.3)
## RcppZiggurat 0.1.6 2020-10-20 [2] CRAN (R 4.1.0)
## RCurl 1.98-1.12 2023-03-27 [2] CRAN (R 4.1.2)
## Rdpack 2.4 2022-07-20 [2] CRAN (R 4.1.2)
## readr * 2.1.4 2023-02-10 [2] CRAN (R 4.1.2)
## readxl * 1.4.3 2023-07-06 [2] CRAN (R 4.1.3)
## remotes 2.4.2 2021-11-30 [2] CRAN (R 4.1.0)
## reshape2 1.4.4 2020-04-09 [2] CRAN (R 4.1.0)
## reticulate 1.30 2023-06-09 [2] CRAN (R 4.1.3)
## Rfast 2.0.8 2023-07-03 [2] CRAN (R 4.1.3)
## rhdf5 2.38.1 2022-03-10 [2] Bioconductor
## rhdf5filters 1.6.0 2021-10-26 [2] Bioconductor
## Rhdf5lib 1.16.0 2021-10-26 [2] Bioconductor
## rlang 1.1.1 2023-04-28 [1] CRAN (R 4.1.2)
## rmarkdown 2.23 2023-07-01 [2] CRAN (R 4.1.3)
## robustbase 0.99-0 2023-06-16 [2] CRAN (R 4.1.3)
## rootSolve 1.8.2.3 2021-09-29 [2] CRAN (R 4.1.0)
## rpart 4.1.19 2022-10-21 [2] CRAN (R 4.1.2)
## RSpectra 0.16-1 2022-04-24 [2] CRAN (R 4.1.2)
## RSQLite 2.3.1 2023-04-03 [2] CRAN (R 4.1.2)
## rstatix 0.7.2 2023-02-01 [2] CRAN (R 4.1.2)
## rstudioapi 0.15.0 2023-07-07 [2] CRAN (R 4.1.3)
## Rtsne 0.16 2022-04-17 [2] CRAN (R 4.1.2)
## RVenn 1.1.0 2019-07-18 [2] CRAN (R 4.1.0)
## rvest 1.0.3 2022-08-19 [2] CRAN (R 4.1.2)
## S4Vectors * 0.32.4 2022-03-29 [2] Bioconductor
## sandwich 3.0-2 2022-06-15 [2] CRAN (R 4.1.2)
## sass 0.4.6 2023-05-03 [2] CRAN (R 4.1.2)
## scales 1.2.1 2022-08-20 [2] CRAN (R 4.1.2)
## scatterplot3d 0.3-44 2023-05-05 [2] CRAN (R 4.1.2)
## sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.1.0)
## sf 1.0-7 2022-03-07 [2] CRAN (R 4.1.2)
## shape 1.4.6 2021-05-19 [2] CRAN (R 4.1.0)
## shiny 1.7.4.1 2023-07-06 [2] CRAN (R 4.1.3)
## sjlabelled 1.2.0 2022-04-10 [2] CRAN (R 4.1.2)
## sjmisc 2.8.9 2021-12-03 [2] CRAN (R 4.1.0)
## snow 0.4-4 2021-10-27 [2] CRAN (R 4.1.0)
## SpiecEasi * 1.1.2 2022-07-14 [2] Github (zdk123/SpiecEasi@c463727)
## SPRING 1.0.4 2022-08-03 [2] Github (GraceYoon/SPRING@3d641a4)
## stringi 1.7.12 2023-01-11 [2] CRAN (R 4.1.2)
## stringr 1.5.0 2022-12-02 [2] CRAN (R 4.1.2)
## SummarizedExperiment * 1.24.0 2021-10-26 [2] Bioconductor
## survival 3.5-5 2023-03-12 [2] CRAN (R 4.1.2)
## svglite 2.1.1 2023-01-10 [2] CRAN (R 4.1.2)
## systemfonts 1.0.4 2022-02-11 [2] CRAN (R 4.1.2)
## tensorA 0.36.2 2020-11-19 [2] CRAN (R 4.1.0)
## TH.data 1.1-2 2023-04-17 [2] CRAN (R 4.1.2)
## tibble * 3.2.1 2023-03-20 [2] CRAN (R 4.1.2)
## tidyr * 1.3.0 2023-01-24 [2] CRAN (R 4.1.2)
## tidyselect 1.2.0 2022-10-10 [2] CRAN (R 4.1.2)
## timechange 0.2.0 2023-01-11 [2] CRAN (R 4.1.2)
## truncnorm 1.0-9 2023-03-20 [2] CRAN (R 4.1.2)
## tzdb 0.4.0 2023-05-12 [2] CRAN (R 4.1.3)
## umap 0.2.10.0 2023-02-01 [2] CRAN (R 4.1.2)
## units 0.8-2 2023-04-27 [2] CRAN (R 4.1.2)
## urlchecker 1.0.1 2021-11-30 [2] CRAN (R 4.1.0)
## usethis * 2.2.2 2023-07-06 [2] CRAN (R 4.1.3)
## utf8 1.2.3 2023-01-31 [2] CRAN (R 4.1.2)
## uuid 1.1-0 2022-04-19 [2] CRAN (R 4.1.2)
## vctrs 0.6.3 2023-06-14 [1] CRAN (R 4.1.3)
## vegan * 2.6-4 2022-10-11 [2] CRAN (R 4.1.2)
## VennDiagram * 1.7.3 2022-04-12 [2] CRAN (R 4.1.2)
## VGAM 1.1-8 2023-03-09 [2] CRAN (R 4.1.2)
## viridis * 0.6.3 2023-05-03 [2] CRAN (R 4.1.2)
## viridisLite * 0.4.2 2023-05-02 [2] CRAN (R 4.1.2)
## vroom 1.6.3 2023-04-28 [2] CRAN (R 4.1.2)
## webshot 0.5.5 2023-06-26 [2] CRAN (R 4.1.3)
## WGCNA 1.72-1 2023-01-18 [2] CRAN (R 4.1.2)
## withr 2.5.0 2022-03-03 [2] CRAN (R 4.1.2)
## Wrench 1.12.0 2021-10-26 [2] Bioconductor
## xfun 0.40 2023-08-09 [1] CRAN (R 4.1.3)
## XMAS2 * 2.2.0 2023-10-27 [1] local
## XML 3.99-0.14 2023-03-19 [2] CRAN (R 4.1.2)
## xml2 1.3.5 2023-07-06 [2] CRAN (R 4.1.3)
## xtable 1.8-4 2019-04-21 [2] CRAN (R 4.1.0)
## XVector 0.34.0 2021-10-26 [2] Bioconductor
## yaml 2.3.7 2023-01-23 [2] CRAN (R 4.1.2)
## zCompositions 1.4.0-1 2022-03-26 [2] CRAN (R 4.1.2)
## zlibbioc 1.40.0 2021-10-26 [2] Bioconductor
## zoo 1.8-12 2023-04-13 [2] CRAN (R 4.1.2)
##
## [1] /Users/zouhua/Library/R/x86_64/4.1/library
## [2] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
##
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────