benchmark/benchmarking.md
In thomazbastiaanssen/kronos: Microbiome Oriented Circadian Rhythm Analysis Toolkit
Preparation
Here, we will compare the performance of Kronos to that of three common
R-based tools to assess rhythmic data. All code available at
https://github.com/thomazbastiaanssen/kronos/blob/main/benchmark/
First, we will load the required packages.
#Wrangling
library(tidyverse)
#Plotting
library(ggforce)
library(ggvenn)
library(UpSetR)
#Load circadian rhythm packages
library(kronos) #devtools::install_github("thomazbastiaanssen/kronos")
library(limorhyde)
library(cosinor)
library(cosinor2)
Now we will load and prepare our high dimensional microbiome data for
assessment.
source("00_load_and_clean_WGS.R")
Next, we apply the four packages to the data. Code to run JTK_CYCLE,
Limorhyde and Cosinor2 was adapted from their respective vignettes.
source("01a_run_kronos.R")
source("01b_run_jtk_cycle.R")
source("01c_run_limorhyde.R")
source("01d_run_cosinor2.R")
Here, we collate all outcome parameters into a single object to compare
them.
res_tot = do.call(cbind, list(res_kronos, res_jtk, res_limo, res_cosinor2))
colnames(res_tot) = paste(colnames(res_tot), c(rep("kronos", ncol(res_kronos)),
rep("jtk", ncol(res_jtk)),
rep("limo", ncol(res_limo)),
rep("cosinor2", ncol(res_cosinor2))),
sep = "_")
Comparing p-value distributions between programs
Theoretically, we expect a uniform distribution between 0-1 (for the
cases where H0 is true) as well as an inflation of low
p-values (for the cases where H1 is true).
par(mfcol = c(2, 2))
hist(res_kronos$p.val, breaks = 20)
hist(res_jtk$p.val, breaks = 20)
hist(res_cosinor2$p.val, breaks = 20)
hist(res_limo$p.val, breaks = 20)
mtext("P-value histograms", side = 3, line = -1, outer = TRUE)
Both Limorhyde and Kronos show a desirable distribution of p-values,
whereas JTK_CYCLE has an inflation on the higher end and Cosinor2 has a
skewed, non-uniform distribution in the H0 region.
Comparing acrophases between programs
res_tot %>%
rownames_to_column("ID") %>%
dplyr::select(!gene_id_limo) %>%
group_by(ID) %>%
filter(min(p.val_kronos,p.val_limo,p.val_jtk,p.val_cosinor2) < 0.05) %>%
ungroup() %>%
ggplot() +
aes(x = .panel_x, y = .panel_y) +
geom_point(aes(x = .panel_x, y = .panel_y)) +
ggforce::facet_matrix(vars(acro_kronos, acro_jtk, acro_cosinor2)) +
theme_bw() +
ggtitle("Concordance in acrophase detection between Kronos, JTK_CYCLE and Cosinor2")
All three programs that produce acrophases are in agreement as to where
the acrophases of features foudn to be rhythmic at p \< 0.05 at least
once are. Limorhyde does not have a clear method to return acrophases.
Plot agreement in hits between programs
In the venn diagram we see how many features are considered hits (p \<
0.05) by the respective programs Alternatively, the UpSetR plot below
shows the same.
venn_plot <- list(kronos = row.names(res_tot[res_tot$p.val_kronos < 0.05,]),
jtk_cycle = row.names(res_tot[res_tot$p.val_jtk < 0.05,]),
limorhyde = row.names(res_tot[res_tot$p.val_limo < 0.05,]),
cosinor2 = row.names(res_tot[res_tot$p.val_cosinor2 < 0.05,])) %>%
ggvenn::ggvenn(text_size = 2.5) +
ggtitle("Venn diagram showing agreement between\nfeatures rhythmic at p < 0.05")
venn_plot$layers[[3]]$data$x <- c(-1, -0.8, 0.8, 1) #adjust margins
venn_plot
list(kronos = row.names(res_tot[res_tot$p.val_kronos < 0.05,]),
jtk_cycle = row.names(res_tot[res_tot$p.val_jtk < 0.05,]),
limorhyde = row.names(res_tot[res_tot$p.val_limo < 0.05,]),
cosinor2 = row.names(res_tot[res_tot$p.val_cosinor2 < 0.05,])) %>%
UpSetR::fromList() %>%
UpSetR::upset(., order.by = "freq",
mainbar.y.label = "Number of p-values < 0.05\n per intersection",
sets.x.label = "Number of p-values < 0.05\n per program")
We can see that Kronos never reports a significntly rhythmic feature
that at least one other program doesn’t also see. Furthermore, Kronos
finds the second highest total number of rhythmic features at p \< 0.05.
Only Cosinor2 finds more hits that Kronos, but 303 of those are not
corroborated by any other tool and thus may be spurious.
From this, we can conclude that Kronos performs as well as (or better
than) the best comparable program in each category. Furthermore, Kronos
allows for convenient testing of arbitrarily complex models and comes
with pre-designed ggplot-compatible plotting functions.
Session Info
sessioninfo::session_info()
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.2.2 Patched (2022-11-10 r83330)
## os Ubuntu 18.04.6 LTS
## system x86_64, linux-gnu
## ui X11
## language en_IE:en
## collate en_IE.UTF-8
## ctype en_IE.UTF-8
## tz Europe/Dublin
## date 2023-04-25
## pandoc 2.19.2 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## annotate 1.74.0 2022-04-26 [1] Bioconductor
## AnnotationDbi 1.58.0 2022-04-26 [1] Bioconductor
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0)
## backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0)
## base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.2.0)
## Biobase 2.56.0 2022-04-26 [1] Bioconductor
## BiocGenerics 0.42.0 2022-04-26 [1] Bioconductor
## Biostrings 2.64.1 2022-08-18 [1] Bioconductor
## bit 4.0.5 2022-11-15 [1] CRAN (R 4.2.1)
## bit64 4.0.5 2020-08-30 [1] CRAN (R 4.2.0)
## bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0)
## blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.0)
## broom 1.0.2 2022-12-15 [1] CRAN (R 4.2.1)
## cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0)
## cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.2.0)
## checkmate 2.1.0 2022-04-21 [1] CRAN (R 4.2.0)
## cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.1)
## cluster 2.1.4 2022-08-22 [4] CRAN (R 4.2.1)
## colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0)
## cosinor * 1.2.2 2022-05-24 [1] CRAN (R 4.2.2)
## cosinor2 * 0.2.1 2018-10-15 [1] CRAN (R 4.2.0)
## cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.2.0)
## crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.1)
## data.table 1.14.6 2022-11-16 [1] CRAN (R 4.2.1)
## DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
## dbplyr 2.3.0 2023-01-16 [1] CRAN (R 4.2.1)
## deldir 1.0-6 2021-10-23 [1] CRAN (R 4.2.1)
## deleuze * 0.1.0.0 2023-01-11 [1] Github (thomazbastiaanssen/deleuze@129f472)
## digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.1)
## dplyr * 1.0.10 2022-09-01 [1] CRAN (R 4.2.1)
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
## evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.1)
## fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
## farver 2.1.1 2022-07-06 [1] CRAN (R 4.2.1)
## fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
## forcats * 0.5.2 2022-08-19 [1] CRAN (R 4.2.1)
## foreign 0.8-82 2022-01-13 [4] CRAN (R 4.1.2)
## Formula 1.2-4 2020-10-16 [1] CRAN (R 4.2.0)
## fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0)
## gargle 1.2.1 2022-09-08 [1] CRAN (R 4.2.1)
## genefilter 1.78.0 2022-04-26 [1] Bioconductor
## generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.1)
## GenomeInfoDb 1.32.4 2022-09-06 [1] Bioconductor
## GenomeInfoDbData 1.2.8 2022-05-09 [1] Bioconductor
## ggforce * 0.4.1 2022-10-04 [1] CRAN (R 4.2.1)
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## ggvenn * 0.1.9 2021-06-29 [1] CRAN (R 4.2.2)
## glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
## googledrive 2.0.0 2021-07-08 [1] CRAN (R 4.2.0)
## googlesheets4 1.0.1 2022-08-13 [1] CRAN (R 4.2.1)
## gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.0)
## gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.1)
## haven 2.5.1 2022-08-22 [1] CRAN (R 4.2.1)
## highr 0.10 2022-12-22 [1] CRAN (R 4.2.1)
## Hmisc 4.7-2 2022-11-18 [1] CRAN (R 4.2.1)
## hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.1)
## htmlTable 2.4.1 2022-07-07 [1] CRAN (R 4.2.1)
## htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.1)
## htmlwidgets 1.6.1 2023-01-07 [1] CRAN (R 4.2.1)
## httpuv 1.6.8 2023-01-12 [1] CRAN (R 4.2.1)
## httr 1.4.4 2022-08-17 [1] CRAN (R 4.2.1)
## interp 1.1-3 2022-07-13 [1] CRAN (R 4.2.1)
## IRanges 2.30.1 2022-08-18 [1] Bioconductor
## jpeg 0.1-10 2022-11-29 [1] CRAN (R 4.2.1)
## jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.2.1)
## KEGGREST 1.36.3 2022-07-12 [1] Bioconductor
## knitr 1.41 2022-11-18 [1] CRAN (R 4.2.1)
## kronos * 0.1.0.0 2023-03-08 [1] Github (thomazbastiaanssen/kronos@4e9a18c)
## labeling 0.4.2 2020-10-20 [1] CRAN (R 4.2.0)
## later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0)
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## lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.1)
## limorhyde * 1.0.1 2022-02-18 [1] CRAN (R 4.2.2)
## lubridate 1.9.0 2022-11-06 [1] CRAN (R 4.2.1)
## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
## MASS 7.3-58.2 2023-01-23 [4] CRAN (R 4.2.2)
## Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.2.1)
## matrixStats 0.63.0 2022-11-18 [1] CRAN (R 4.2.1)
## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
## mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
## modelr 0.1.10 2022-11-11 [1] CRAN (R 4.2.1)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
## nnet 7.3-18 2022-09-28 [4] CRAN (R 4.2.1)
## pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
## plyr 1.8.8 2022-11-11 [1] CRAN (R 4.2.1)
## png 0.1-8 2022-11-29 [1] CRAN (R 4.2.1)
## polyclip 1.10-4 2022-10-20 [1] CRAN (R 4.2.1)
## promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0)
## purrr * 1.0.1 2023-01-10 [1] CRAN (R 4.2.1)
## R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
## RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.2.0)
## Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.1)
## RCurl 1.98-1.9 2022-10-03 [1] CRAN (R 4.2.1)
## readr * 2.1.3 2022-10-01 [1] CRAN (R 4.2.1)
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## rpart 4.1.19 2022-10-21 [4] CRAN (R 4.2.1)
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## rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
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## S4Vectors 0.34.0 2022-04-26 [1] Bioconductor
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## tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.0)
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## zlibbioc 1.42.0 2022-04-26 [1] Bioconductor
##
## [1] /home/thomaz/R/x86_64-pc-linux-gnu-library/4.2
## [2] /usr/local/lib/R/site-library
## [3] /usr/lib/R/site-library
## [4] /usr/lib/R/library
##
## ──────────────────────────────────────────────────────────────────────────────
thomazbastiaanssen/kronos documentation built on May 1, 2023, 6:45 p.m.
R Package Documentation
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Preparation
Here, we will compare the performance of Kronos to that of three common R-based tools to assess rhythmic data. All code available at https://github.com/thomazbastiaanssen/kronos/blob/main/benchmark/
First, we will load the required packages.
#Wrangling
library(tidyverse)
#Plotting
library(ggforce)
library(ggvenn)
library(UpSetR)
#Load circadian rhythm packages
library(kronos) #devtools::install_github("thomazbastiaanssen/kronos")
library(limorhyde)
library(cosinor)
library(cosinor2)
Now we will load and prepare our high dimensional microbiome data for assessment.
source("00_load_and_clean_WGS.R")
Next, we apply the four packages to the data. Code to run JTK_CYCLE, Limorhyde and Cosinor2 was adapted from their respective vignettes.
source("01a_run_kronos.R")
source("01b_run_jtk_cycle.R")
source("01c_run_limorhyde.R")
source("01d_run_cosinor2.R")
Here, we collate all outcome parameters into a single object to compare them.
res_tot = do.call(cbind, list(res_kronos, res_jtk, res_limo, res_cosinor2))
colnames(res_tot) = paste(colnames(res_tot), c(rep("kronos", ncol(res_kronos)),
rep("jtk", ncol(res_jtk)),
rep("limo", ncol(res_limo)),
rep("cosinor2", ncol(res_cosinor2))),
sep = "_")
Comparing p-value distributions between programs
Theoretically, we expect a uniform distribution between 0-1 (for the cases where H0 is true) as well as an inflation of low p-values (for the cases where H1 is true).
par(mfcol = c(2, 2))
hist(res_kronos$p.val, breaks = 20)
hist(res_jtk$p.val, breaks = 20)
hist(res_cosinor2$p.val, breaks = 20)
hist(res_limo$p.val, breaks = 20)
mtext("P-value histograms", side = 3, line = -1, outer = TRUE)
Both Limorhyde and Kronos show a desirable distribution of p-values, whereas JTK_CYCLE has an inflation on the higher end and Cosinor2 has a skewed, non-uniform distribution in the H0 region.
Comparing acrophases between programs
res_tot %>%
rownames_to_column("ID") %>%
dplyr::select(!gene_id_limo) %>%
group_by(ID) %>%
filter(min(p.val_kronos,p.val_limo,p.val_jtk,p.val_cosinor2) < 0.05) %>%
ungroup() %>%
ggplot() +
aes(x = .panel_x, y = .panel_y) +
geom_point(aes(x = .panel_x, y = .panel_y)) +
ggforce::facet_matrix(vars(acro_kronos, acro_jtk, acro_cosinor2)) +
theme_bw() +
ggtitle("Concordance in acrophase detection between Kronos, JTK_CYCLE and Cosinor2")
All three programs that produce acrophases are in agreement as to where the acrophases of features foudn to be rhythmic at p \< 0.05 at least once are. Limorhyde does not have a clear method to return acrophases.
Plot agreement in hits between programs
In the venn diagram we see how many features are considered hits (p \< 0.05) by the respective programs Alternatively, the UpSetR plot below shows the same.
venn_plot <- list(kronos = row.names(res_tot[res_tot$p.val_kronos < 0.05,]),
jtk_cycle = row.names(res_tot[res_tot$p.val_jtk < 0.05,]),
limorhyde = row.names(res_tot[res_tot$p.val_limo < 0.05,]),
cosinor2 = row.names(res_tot[res_tot$p.val_cosinor2 < 0.05,])) %>%
ggvenn::ggvenn(text_size = 2.5) +
ggtitle("Venn diagram showing agreement between\nfeatures rhythmic at p < 0.05")
venn_plot$layers[[3]]$data$x <- c(-1, -0.8, 0.8, 1) #adjust margins
venn_plot
list(kronos = row.names(res_tot[res_tot$p.val_kronos < 0.05,]),
jtk_cycle = row.names(res_tot[res_tot$p.val_jtk < 0.05,]),
limorhyde = row.names(res_tot[res_tot$p.val_limo < 0.05,]),
cosinor2 = row.names(res_tot[res_tot$p.val_cosinor2 < 0.05,])) %>%
UpSetR::fromList() %>%
UpSetR::upset(., order.by = "freq",
mainbar.y.label = "Number of p-values < 0.05\n per intersection",
sets.x.label = "Number of p-values < 0.05\n per program")
We can see that Kronos never reports a significntly rhythmic feature that at least one other program doesn’t also see. Furthermore, Kronos finds the second highest total number of rhythmic features at p \< 0.05. Only Cosinor2 finds more hits that Kronos, but 303 of those are not corroborated by any other tool and thus may be spurious.
From this, we can conclude that Kronos performs as well as (or better than) the best comparable program in each category. Furthermore, Kronos allows for convenient testing of arbitrarily complex models and comes with pre-designed ggplot-compatible plotting functions.
Session Info
sessioninfo::session_info()
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.2.2 Patched (2022-11-10 r83330)
## os Ubuntu 18.04.6 LTS
## system x86_64, linux-gnu
## ui X11
## language en_IE:en
## collate en_IE.UTF-8
## ctype en_IE.UTF-8
## tz Europe/Dublin
## date 2023-04-25
## pandoc 2.19.2 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## annotate 1.74.0 2022-04-26 [1] Bioconductor
## AnnotationDbi 1.58.0 2022-04-26 [1] Bioconductor
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0)
## backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0)
## base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.2.0)
## Biobase 2.56.0 2022-04-26 [1] Bioconductor
## BiocGenerics 0.42.0 2022-04-26 [1] Bioconductor
## Biostrings 2.64.1 2022-08-18 [1] Bioconductor
## bit 4.0.5 2022-11-15 [1] CRAN (R 4.2.1)
## bit64 4.0.5 2020-08-30 [1] CRAN (R 4.2.0)
## bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0)
## blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.0)
## broom 1.0.2 2022-12-15 [1] CRAN (R 4.2.1)
## cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0)
## cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.2.0)
## checkmate 2.1.0 2022-04-21 [1] CRAN (R 4.2.0)
## cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.1)
## cluster 2.1.4 2022-08-22 [4] CRAN (R 4.2.1)
## colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0)
## cosinor * 1.2.2 2022-05-24 [1] CRAN (R 4.2.2)
## cosinor2 * 0.2.1 2018-10-15 [1] CRAN (R 4.2.0)
## cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.2.0)
## crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.1)
## data.table 1.14.6 2022-11-16 [1] CRAN (R 4.2.1)
## DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
## dbplyr 2.3.0 2023-01-16 [1] CRAN (R 4.2.1)
## deldir 1.0-6 2021-10-23 [1] CRAN (R 4.2.1)
## deleuze * 0.1.0.0 2023-01-11 [1] Github (thomazbastiaanssen/deleuze@129f472)
## digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.1)
## dplyr * 1.0.10 2022-09-01 [1] CRAN (R 4.2.1)
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
## evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.1)
## fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
## farver 2.1.1 2022-07-06 [1] CRAN (R 4.2.1)
## fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
## forcats * 0.5.2 2022-08-19 [1] CRAN (R 4.2.1)
## foreign 0.8-82 2022-01-13 [4] CRAN (R 4.1.2)
## Formula 1.2-4 2020-10-16 [1] CRAN (R 4.2.0)
## fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0)
## gargle 1.2.1 2022-09-08 [1] CRAN (R 4.2.1)
## genefilter 1.78.0 2022-04-26 [1] Bioconductor
## generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.1)
## GenomeInfoDb 1.32.4 2022-09-06 [1] Bioconductor
## GenomeInfoDbData 1.2.8 2022-05-09 [1] Bioconductor
## ggforce * 0.4.1 2022-10-04 [1] CRAN (R 4.2.1)
## ggplot2 * 3.4.0 2022-11-04 [1] CRAN (R 4.2.1)
## ggvenn * 0.1.9 2021-06-29 [1] CRAN (R 4.2.2)
## glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
## googledrive 2.0.0 2021-07-08 [1] CRAN (R 4.2.0)
## googlesheets4 1.0.1 2022-08-13 [1] CRAN (R 4.2.1)
## gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.0)
## gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.1)
## haven 2.5.1 2022-08-22 [1] CRAN (R 4.2.1)
## highr 0.10 2022-12-22 [1] CRAN (R 4.2.1)
## Hmisc 4.7-2 2022-11-18 [1] CRAN (R 4.2.1)
## hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.1)
## htmlTable 2.4.1 2022-07-07 [1] CRAN (R 4.2.1)
## htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.1)
## htmlwidgets 1.6.1 2023-01-07 [1] CRAN (R 4.2.1)
## httpuv 1.6.8 2023-01-12 [1] CRAN (R 4.2.1)
## httr 1.4.4 2022-08-17 [1] CRAN (R 4.2.1)
## interp 1.1-3 2022-07-13 [1] CRAN (R 4.2.1)
## IRanges 2.30.1 2022-08-18 [1] Bioconductor
## jpeg 0.1-10 2022-11-29 [1] CRAN (R 4.2.1)
## jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.2.1)
## KEGGREST 1.36.3 2022-07-12 [1] Bioconductor
## knitr 1.41 2022-11-18 [1] CRAN (R 4.2.1)
## kronos * 0.1.0.0 2023-03-08 [1] Github (thomazbastiaanssen/kronos@4e9a18c)
## labeling 0.4.2 2020-10-20 [1] CRAN (R 4.2.0)
## later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0)
## lattice 0.20-45 2021-09-22 [4] CRAN (R 4.2.0)
## latticeExtra 0.6-30 2022-07-04 [1] CRAN (R 4.2.1)
## lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.1)
## limorhyde * 1.0.1 2022-02-18 [1] CRAN (R 4.2.2)
## lubridate 1.9.0 2022-11-06 [1] CRAN (R 4.2.1)
## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
## MASS 7.3-58.2 2023-01-23 [4] CRAN (R 4.2.2)
## Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.2.1)
## matrixStats 0.63.0 2022-11-18 [1] CRAN (R 4.2.1)
## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
## mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
## modelr 0.1.10 2022-11-11 [1] CRAN (R 4.2.1)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
## nnet 7.3-18 2022-09-28 [4] CRAN (R 4.2.1)
## pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
## plyr 1.8.8 2022-11-11 [1] CRAN (R 4.2.1)
## png 0.1-8 2022-11-29 [1] CRAN (R 4.2.1)
## polyclip 1.10-4 2022-10-20 [1] CRAN (R 4.2.1)
## promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0)
## purrr * 1.0.1 2023-01-10 [1] CRAN (R 4.2.1)
## R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
## RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.2.0)
## Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.1)
## RCurl 1.98-1.9 2022-10-03 [1] CRAN (R 4.2.1)
## readr * 2.1.3 2022-10-01 [1] CRAN (R 4.2.1)
## readxl 1.4.1 2022-08-17 [1] CRAN (R 4.2.1)
## reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1)
## rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
## rmarkdown 2.20 2023-01-19 [1] CRAN (R 4.2.1)
## rpart 4.1.19 2022-10-21 [4] CRAN (R 4.2.1)
## RSQLite 2.2.20 2022-12-22 [1] CRAN (R 4.2.1)
## rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
## rvest 1.0.3 2022-08-19 [1] CRAN (R 4.2.1)
## S4Vectors 0.34.0 2022-04-26 [1] Bioconductor
## scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.1)
## sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
## shiny 1.7.4 2022-12-15 [1] CRAN (R 4.2.1)
## stringi 1.7.12 2023-01-11 [1] CRAN (R 4.2.1)
## stringr * 1.5.0 2022-12-02 [1] CRAN (R 4.2.1)
## survival 3.4-0 2022-08-09 [4] CRAN (R 4.2.1)
## tibble * 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
## tidyr * 1.2.1 2022-09-08 [1] CRAN (R 4.2.1)
## tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.1)
## tidyverse * 1.3.2 2022-07-18 [1] CRAN (R 4.2.1)
## timechange 0.2.0 2023-01-11 [1] CRAN (R 4.2.1)
## tweenr 2.0.2 2022-09-06 [1] CRAN (R 4.2.1)
## tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.0)
## UpSetR * 1.4.0 2019-05-22 [1] CRAN (R 4.2.2)
## utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
## vctrs 0.5.1 2022-11-16 [1] CRAN (R 4.2.1)
## withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
## xfun 0.36 2022-12-21 [1] CRAN (R 4.2.1)
## XML 3.99-0.13 2022-12-04 [1] CRAN (R 4.2.1)
## xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0)
## xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0)
## XVector 0.36.0 2022-04-26 [1] Bioconductor
## yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.1)
## zlibbioc 1.42.0 2022-04-26 [1] Bioconductor
##
## [1] /home/thomaz/R/x86_64-pc-linux-gnu-library/4.2
## [2] /usr/local/lib/R/site-library
## [3] /usr/lib/R/site-library
## [4] /usr/lib/R/library
##
## ──────────────────────────────────────────────────────────────────────────────
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