H3K9me3 and TE overlap
Renee Matthews
2026-02-02
Last updated: 2026-02-02
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Knit directory: DXR_continue/
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library(tidyverse)
library(GenomicRanges)
library(plyranges)
library(genomation)
library(readr)
library(rtracklayer)
library(stringr)
library(ggrepel)
library(DT)
library(ChIPseeker)
library(ggVennDiagram)
library(smplot2)First steps: breakdown repeatmasker into groups and pull out the ones by each class I am interested in.
repeatmasker <- read_delim("data/Other_paper_data/repeatmasker_20250911.txt",
delim = "\t", escape_double = FALSE,
trim_ws = TRUE)
colnames(repeatmasker) [1] "#bin" "swScore" "milliDiv" "milliDel" "milliIns" "genoName"
[7] "genoStart" "genoEnd" "genoLeft" "strand" "repName" "repClass"
[13] "repFamily" "repStart" "repEnd" "repLeft" "id" autosomes <- paste0("chr", 1:22)
repeatmasker_clean <- repeatmasker %>% mutate(
strand = ifelse(strand == "C", "-", "+")
) %>%
mutate(
start = genoStart + 1,
end = genoEnd)%>%
mutate(repFamily= str_remove(repFamily, "\\?$")) %>%
dplyr::filter(genoName %in% autosomes) %>%
mutate(RM_id=paste0(genoName,":",start,"-",end,":",id))
rpt_split <- split(repeatmasker_clean, repeatmasker_clean$repClass)
rpt_split_gr_list <- lapply(rpt_split, function(df) {
GRanges(
seqnames = df$genoName,
ranges = IRanges(start = df$start, end = df$end),
strand = df$strand,
repName = df$repName,
repClass = df$repClass,
repFamily = df$repFamily,
swScore = df$swScore,
milliDiv = df$milliDiv,
milliDel = df$milliDel,
milliIns = df$milliIns,
RM_id = df$RM_id
)
})SINE_gr <- rpt_split_gr_list$SINE
SINE_df <- SINE_gr %>%
as.data.frame()
SINE_split_df <- split(SINE_df, SINE_df$repFamily)
LINE_gr <- rpt_split_gr_list$LINE
LINE_df <- LINE_gr %>%
as.data.frame()
LINE_split_df <- split(LINE_df, LINE_df$repFamily)
LTR_gr <- rpt_split_gr_list$LTR
LTR_df <- LTR_gr %>%
as.data.frame()
LTR_split_df <- split(LTR_df, LTR_df$repFamily)
SVA_gr <- rpt_split_gr_list$Retroposon
SVA_df <- SVA_gr %>%
as.data.frame()
SVA_split_df <- split(SVA_df, SVA_df$repFamily)
DNA_gr <- rpt_split_gr_list$DNA
DNA_df <- DNA_gr %>%
as.data.frame()
DNA_split_df <- split(DNA_df, DNA_df$repFamily)H3K9me3_summit_gr <- readRDS("data/RDS_files/H3K9me3_complete_summit_gr.RDS")
peakAnnoList_H3K27ac <- readRDS("data/motif_lists/H3K27ac_annotated_peaks.RDS")
peakAnnoList_H3K9me3 <- readRDS("data/motif_lists/H3K9me3_annotated_peaks.RDS")
H3K27ac_lookup <- imap_dfr(peakAnnoList_H3K27ac[1:3], ~
tibble(Peakid = .x@anno$Peakid, cluster = .y))
H3K9me3_lookup <- imap_dfr(peakAnnoList_H3K9me3[1:3], ~
tibble(Peakid = .x@anno$Peakid, cluster = .y))
H3K27ac_sets_gr <- lapply(peakAnnoList_H3K27ac, function(df) {
as_granges(df)
})
H3K9me3_sets_gr <- lapply(peakAnnoList_H3K9me3, function(df) {
as_granges(df)
})
##assigning Peakid as name of summit region
mcols(H3K9me3_summit_gr)$name <- mcols(H3K9me3_summit_gr)$Peakid
comparisons <- tibble(
cluster2 = c("Set_2", "Set_3"),
cluster1 = c("Set_1", "Set_1")
)H3K9me3_toplist <- readRDS( "data/DER_data/H3K9me3_toplist_nooutlier.RDS")
H3K27ac_toplist <- readRDS( "data/DER_data/H3K27ac_toplist.RDS")
H3K27ac_toptable_list <- bind_rows(H3K27ac_toplist, .id = "group")
H3K9me3_toptable_list <- bind_rows(H3K9me3_toplist, .id = "group")
K9me3_lfctable <- H3K9me3_toptable_list %>%
dplyr::select(group,genes, logFC) %>%
pivot_wider(.,id_cols = genes, names_from = group, values_from = logFC)
K27ac_lfctable <- H3K27ac_toptable_list %>%
dplyr::select(group,genes, logFC) %>%
pivot_wider(.,id_cols = genes, names_from = group, values_from = logFC)
cluster_colors <- c("Set_1" = "#d93e40","Set_2" = "#1c9f50","Set_3" = "#3570b3","NA" ="grey70")# Generic pairwise Fisher test
test_pair_TE_generic <- function(df_long, te_name, cluster1, cluster2) {
sub_df <- df_long %>%
filter(TE_type == te_name) %>%
complete(
cluster = c(cluster1, cluster2),
status = c("TE", "not_TE"),
fill = list(count = 0))
# enforce fixed order
status_levels <- c("TE", "not_TE")
# assume "status" column has TE vs wnot_TE automatically
statuses <- unique(sub_df$status)
if(length(statuses) != 2) {
# ensure we have exactly two categories, fill missing with 0
sub_df <- sub_df %>%
complete(cluster, status, fill = list(count = 0))
statuses <- unique(sub_df$status)
}
# extract counts for cluster1
c1_counts <- sub_df %>%
filter(cluster == cluster1) %>%
arrange(factor(status, levels = status_levels)) %>% # ensure same order
pull(count)
# extract counts for cluster2
c2_counts <- sub_df %>%
filter(cluster == cluster2) %>%
arrange(factor(status, levels = status_levels)) %>%
pull(count)
# build 2x2 matrix
mat <- matrix(
c(c2_counts, c1_counts),
nrow = 2,
byrow = TRUE,
dimnames = list(
cluster = c(cluster2, cluster1),
category = status_levels
)
)
ft <- tryCatch(
fisher.test(mat, workspace = 2e8),
error = function(e) fisher.test(mat, simulate.p.value = TRUE, B = 1e5)
)
tibble(
TE_type = te_name,
comparison = paste(cluster2, "vs", cluster1),
odds_ratio = ft$estimate,
lower_CI = ft$conf.int[1],
upper_CI = ft$conf.int[2],
p_value = ft$p.value
)
}SINE
Overlapping SINE family with ROIs
sine_hits <- findOverlaps(H3K9me3_sets_gr$all_H3K9me3, SINE_gr, ignore.strand = TRUE)
SINE_overlap_df <- tibble(
peak_row = queryHits(sine_hits),
Peakid = H3K9me3_sets_gr$all_H3K9me3$Peakid[queryHits(sine_hits)],
cluster = H3K9me3_sets_gr$all_H3K9me3$cluster[queryHits(sine_hits)],
repClass = SINE_gr$repClass[subjectHits(sine_hits)],
repName = SINE_gr$repName[subjectHits(sine_hits)],
TE_type = ifelse(
SINE_gr$repFamily[subjectHits(sine_hits)] == "SVA",
SINE_gr$repName[subjectHits(sine_hits)],
SINE_gr$repFamily[subjectHits(sine_hits)]
),
milliDiv = SINE_gr$milliDiv[subjectHits(sine_hits)],
milliDel = SINE_gr$milliDel[subjectHits(sine_hits)],
milliIns = SINE_gr$milliIns[subjectHits(sine_hits)]
)
SINE_overlap_df %>%
dplyr::left_join(H3K9me3_lookup) %>%
dplyr::filter(cluster %in% c("Set_1","Set_2","Set_3")) %>%
ggplot(., aes(x = TE_type, y = milliDiv)) +
geom_violin(trim = FALSE) +
geom_boxplot(width = 0.15, outlier.shape = NA) +
coord_flip() +
labs(
y = "Divergence from consensus (milliDiv)",
x = "TE family",
title = "Age distribution of SINE elements overlapping H3K9me3"
)+
facet_wrap(~cluster)
| Version | Author | Date |
|---|---|---|
| dc70156 | reneeisnowhere | 2026-02-02 |
SINE_overlap_df %>%
dplyr::left_join(H3K9me3_lookup) %>%
dplyr::filter(cluster %in% c("Set_1","Set_2","Set_3")) %>%
ggplot(., aes(x = cluster, y = milliDiv)) +
geom_violin(trim = FALSE) +
geom_boxplot(width = 0.15, outlier.shape = NA) +
coord_flip() +
labs(
y = "Divergence from consensus (milliDiv)",
x = "TE family",
title = "Age distribution of SINE elements overlapping H3K9me3"
)+
facet_wrap(~repName)
| Version | Author | Date |
|---|---|---|
| dc70156 | reneeisnowhere | 2026-02-02 |
LINE
Overlapping LINE family with ROIs
LINE_hits <- findOverlaps(H3K9me3_sets_gr$all_H3K9me3, LINE_gr, ignore.strand = TRUE)
LINE_overlap_df <- tibble(
peak_row = queryHits(LINE_hits),
Peakid = H3K9me3_sets_gr$all_H3K9me3$Peakid[queryHits(LINE_hits)],
cluster = H3K9me3_sets_gr$all_H3K9me3$cluster[queryHits(LINE_hits)],
repClass = LINE_gr$repClass[subjectHits(LINE_hits)],
repName = LINE_gr$repName[subjectHits(LINE_hits)],
TE_type = ifelse(
LINE_gr$repFamily[subjectHits(LINE_hits)] == "SVA",
LINE_gr$repName[subjectHits(LINE_hits)],
LINE_gr$repFamily[subjectHits(LINE_hits)]
),
milliDiv = LINE_gr$milliDiv[subjectHits(LINE_hits)],
milliDel = LINE_gr$milliDel[subjectHits(LINE_hits)],
milliIns = LINE_gr$milliIns[subjectHits(LINE_hits)]
)
LINE_overlap_df %>%
dplyr::left_join(H3K9me3_lookup) %>%
dplyr::filter(cluster %in% c("Set_1","Set_2","Set_3")) %>%
ggplot(., aes(x = TE_type, y = milliDiv)) +
geom_violin(trim = FALSE) +
geom_boxplot(width = 0.15, outlier.shape = NA) +
coord_flip() +
labs(
y = "Divergence from consensus (milliDiv)",
x = "TE family",
title = "Age distribution of LINE elements overlapping H3K9me3"
)+
facet_wrap(~cluster)
| Version | Author | Date |
|---|---|---|
| dc70156 | reneeisnowhere | 2026-02-02 |
LTR
Overlapping LTR family with ROIs
LTR_hits <- findOverlaps(H3K9me3_sets_gr$all_H3K9me3, LTR_gr, ignore.strand = TRUE)
LTR_overlap_df <- tibble(
peak_row = queryHits(LTR_hits),
Peakid = H3K9me3_sets_gr$all_H3K9me3$Peakid[queryHits(LTR_hits)],
cluster = H3K9me3_sets_gr$all_H3K9me3$cluster[queryHits(LTR_hits)],
repClass = LTR_gr$repClass[subjectHits(LTR_hits)],
repName = LTR_gr$repName[subjectHits(LTR_hits)],
RM_id = LTR_gr$RM_id[subjectHits(LTR_hits)],
TE_type = ifelse(
LTR_gr$repFamily[subjectHits(LTR_hits)] == "SVA",
LTR_gr$repName[subjectHits(LTR_hits)],
LTR_gr$repFamily[subjectHits(LTR_hits)]
),
milliDiv = LTR_gr$milliDiv[subjectHits(LTR_hits)],
milliDel = LTR_gr$milliDel[subjectHits(LTR_hits)],
milliIns = LTR_gr$milliIns[subjectHits(LTR_hits)]
)
LTR_overlap_df %>%
dplyr::left_join(H3K9me3_lookup) %>%
dplyr::filter(cluster %in% c("Set_1","Set_2","Set_3")) %>%
ggplot(., aes(x = TE_type, y = milliDiv)) +
geom_violin(trim = FALSE) +
geom_boxplot(width = 0.15, outlier.shape = NA) +
coord_flip() +
labs(
y = "Divergence from consensus (milliDiv)",
x = "TE family",
title = "Age distribution of LTR elements overlapping H3K9me3"
)+
facet_wrap(~cluster)
| Version | Author | Date |
|---|---|---|
| dc70156 | reneeisnowhere | 2026-02-02 |
DNA
Overlapping DNA family with ROIs
DNA_hits <- findOverlaps(H3K9me3_sets_gr$all_H3K9me3, DNA_gr, ignore.strand = TRUE)
DNA_overlap_df <- tibble(
peak_row = queryHits(DNA_hits),
Peakid = H3K9me3_sets_gr$all_H3K9me3$Peakid[queryHits(DNA_hits)],
cluster = H3K9me3_sets_gr$all_H3K9me3$cluster[queryHits(DNA_hits)],
repClass = DNA_gr$repClass[subjectHits(DNA_hits)],
repName = DNA_gr$repName[subjectHits(DNA_hits)],
TE_type = ifelse(
DNA_gr$repFamily[subjectHits(DNA_hits)] == "SVA",
DNA_gr$repName[subjectHits(DNA_hits)],
DNA_gr$repFamily[subjectHits(DNA_hits)]
),
milliDiv = DNA_gr$milliDiv[subjectHits(DNA_hits)],
milliDel = DNA_gr$milliDel[subjectHits(DNA_hits)],
milliIns = DNA_gr$milliIns[subjectHits(DNA_hits)]
)
DNA_overlap_df %>%
dplyr::left_join(H3K9me3_lookup) %>%
dplyr::filter(cluster %in% c("Set_1","Set_2","Set_3")) %>%
ggplot(., aes(x = TE_type, y = milliDiv)) +
geom_violin(trim = FALSE) +
geom_boxplot(width = 0.15, outlier.shape = NA) +
coord_flip() +
labs(
y = "Divergence from consensus (milliDiv)",
x = "TE family",
title = "Age distribution of DNA elements overlapping H3K9me3"
)+
facet_wrap(~cluster)
| Version | Author | Date |
|---|---|---|
| dc70156 | reneeisnowhere | 2026-02-02 |
SVA/Retroposon
Overlapping SVA family with ROIs
SVA_hits <- findOverlaps(H3K9me3_sets_gr$all_H3K9me3, SVA_gr, ignore.strand = TRUE)
SVA_overlap_df <- tibble(
peak_row = queryHits(SVA_hits),
Peakid = H3K9me3_sets_gr$all_H3K9me3$Peakid[queryHits(SVA_hits)],
cluster = H3K9me3_sets_gr$all_H3K9me3$cluster[queryHits(SVA_hits)],
repClass = SVA_gr$repClass[subjectHits(SVA_hits)],
repName = SVA_gr$repName[subjectHits(SVA_hits)],
TE_type = ifelse(
SVA_gr$repFamily[subjectHits(SVA_hits)] == "SVA",
SVA_gr$repName[subjectHits(SVA_hits)],
SVA_gr$repFamily[subjectHits(SVA_hits)]
),
milliDiv = SVA_gr$milliDiv[subjectHits(SVA_hits)],
milliDel = SVA_gr$milliDel[subjectHits(SVA_hits)],
milliIns = SVA_gr$milliIns[subjectHits(SVA_hits)]
)
SVA_overlap_df %>%
dplyr::left_join(H3K9me3_lookup) %>%
dplyr::filter(cluster %in% c("Set_1","Set_2","Set_3")) %>%
ggplot(., aes(x = TE_type, y = milliDiv)) +
geom_violin(trim = FALSE) +
geom_boxplot(width = 0.15, outlier.shape = NA) +
coord_flip() +
labs(
y = "Divergence from consensus (milliDiv)",
x = "TE family",
title = "Age distribution of SVA elements overlapping H3K9me3"
)+
facet_wrap(~cluster)
| Version | Author | Date |
|---|---|---|
| dc70156 | reneeisnowhere | 2026-02-02 |
Looking for overlapping information: LTR specific
Here I am exploring H3K9me3 ROIs which overlap LTRs and also overlap H3K27ac ROIs, then exploring LFC of the H3K9me3 ROI sets across families of LTRs. First I wanted to know how many H3K9me3 ROIs overlap LTRs, and howmany of those are more than one LTR:
LTR_overlap_df %>%
count(Peakid, name = "n_peaks") %>%
count(n_peaks)# A tibble: 12 × 2
n_peaks n
<int> <int>
1 1 50846
2 2 12180
3 3 2466
4 4 575
5 5 122
6 6 33
7 7 14
8 8 11
9 9 2
10 11 2
11 12 2
12 15 1LTR_only_K27ac_peakids <- LTR_overlap_df %>% distinct(Peakid)I then overlapped ROIs with H3K9me3 ROIs to see how many unique H3K9me3 ROIs are involved.
K27ac_hits <- findOverlaps(H3K9me3_sets_gr$all_H3K9me3_regions, H3K27ac_sets_gr$all_H3K27ac, ignore.strand = TRUE)
K27ac_overlap_df <- tibble(
peak_row = queryHits(K27ac_hits),
Peakid = H3K9me3_sets_gr$all_H3K9me3_regions$Peakid[queryHits(K27ac_hits)],
cluster = H3K9me3_sets_gr$all_H3K9me3_regions$cluster[queryHits(K27ac_hits)],
ROI_K27ac = H3K27ac_sets_gr$all_H3K27ac$Peakid[subjectHits(K27ac_hits)])
K27ac_overlap_df %>%
count(Peakid, name = "n_peaks") %>%
count(n_peaks)# A tibble: 4 × 2
n_peaks n
<int> <int>
1 1 49684
2 2 397
3 3 7
4 4 1K27ac_only_K9me3_peakids <- K27ac_overlap_df %>% distinct(Peakid)Now to filter and connect H3K9me3 ROIs, that overlap LTRs and at least one H3K9me3
LTR_overlap_df %>%
dplyr::filter(Peakid %in% K27ac_only_K9me3_peakids$Peakid) %>% distinct(RM_id)# A tibble: 6,368 × 1
RM_id
<chr>
1 chr1:1003500-1003623:1
2 chr1:1005447-1005607:1
3 chr1:1017170-1018876:1
4 chr1:1235837-1235999:1
5 chr1:1259547-1259908:1
6 chr1:1382090-1382288:1
7 chr1:2097759-2098300:2
8 chr1:2108760-2108974:2
9 chr1:2115428-2116169:2
10 chr1:2124513-2124680:2
# ℹ 6,358 more rowsLFC of those regions
LTR_overlap_df %>%
dplyr::filter(Peakid %in% K27ac_only_K9me3_peakids$Peakid) %>%
left_join(., H3K27ac_lookup) %>%
left_join(., K9me3_lfctable, by = c("Peakid"="genes")) %>%
group_by(TE_type) %>%
tally() %>%
ungroup() %>%
DT::datatable(
rownames = FALSE,
caption = htmltools::tags$caption(
style = "caption-side: top; text-align: left;",
"H3K9me3 LTR specific overlap counts by TE familiy which also overlap H3K27ac"),
options = list(pageLength = 10,
autoWidth = TRUE,
dom = "tip"))LTR_overlap_df %>%
dplyr::left_join(H3K9me3_lookup) %>%
dplyr::filter(Peakid %in% K27ac_only_K9me3_peakids$Peakid) %>%
dplyr::filter(cluster %in% c("Set_1","Set_2","Set_3")) %>%
ggplot(., aes(x = TE_type, y = milliDiv)) +
geom_violin(trim = FALSE) +
geom_boxplot(width = 0.15, outlier.shape = NA) +
coord_flip() +
labs(
y = "Divergence from consensus (milliDiv)",
x = "TE family",
title = "Age distribution of LTR elements overlapping H3K9me3 and H3K27ac"
)+
facet_wrap(~cluster)
| Version | Author | Date |
|---|---|---|
| dc70156 | reneeisnowhere | 2026-02-02 |
LTR_K27ac_H3K9me3_lfc <- LTR_overlap_df %>%
dplyr::left_join(H3K9me3_lookup) %>%
left_join(., K9me3_lfctable, by = c("Peakid"="genes")) %>%
dplyr::filter(Peakid %in% K27ac_only_K9me3_peakids$Peakid)plot_K9_family <- function(lfc_df,
grp="H3K9me3",
repFamily,
fam_name){
lfc_df %>%
dplyr::filter(Peakid %in% K27ac_only_K9me3_peakids$Peakid) %>%
dplyr::filter(.data$TE_type %in% fam_name) %>%
dplyr::filter(cluster != "NA") %>%
pivot_longer(.,cols=c(starts_with(grp)), names_to="group", values_to = "LFC") %>%
group_by(cluster, group) %>%
summarise(median_abs_LFC = median(abs(LFC), na.rm = TRUE),
.groups = "drop")%>%
mutate(time=str_remove(group,grp))%>%
mutate(time=factor(time, levels=c("_24T","_24R","_144R"))) %>%
ggplot(., aes(x=time, y=median_abs_LFC, group=cluster, color=cluster))+
geom_point(size=4)+
geom_line(aes(alpha = 0.8, linewidth = 4))+
theme_bw()+
ggtitle(paste0(grp," absolute LFC overlapping ",repFamily,":",fam_name))
}plot_K9_family(LTR_K27ac_H3K9me3_lfc,"H3K9me3","LTR","ERV1")+
scale_color_manual(values = cluster_colors, drop = FALSE)
| Version | Author | Date |
|---|---|---|
| dc70156 | reneeisnowhere | 2026-02-02 |
plot_K9_family(LTR_K27ac_H3K9me3_lfc,"H3K9me3","LTR","ERVK")+
scale_color_manual(values = cluster_colors, drop = FALSE)
| Version | Author | Date |
|---|---|---|
| dc70156 | reneeisnowhere | 2026-02-02 |
plot_K9_family(LTR_K27ac_H3K9me3_lfc,"H3K9me3","LTR","ERVL")+
scale_color_manual(values = cluster_colors, drop = FALSE)
| Version | Author | Date |
|---|---|---|
| dc70156 | reneeisnowhere | 2026-02-02 |
plot_K9_family(LTR_K27ac_H3K9me3_lfc,"H3K9me3","LTR","Gypsy")+
scale_color_manual(values = cluster_colors, drop = FALSE)
| Version | Author | Date |
|---|---|---|
| dc70156 | reneeisnowhere | 2026-02-02 |
plot_K9_family(LTR_K27ac_H3K9me3_lfc,"H3K9me3","LTR","ERVL-MaLR")+
scale_color_manual(values = cluster_colors, drop = FALSE)
| Version | Author | Date |
|---|---|---|
| dc70156 | reneeisnowhere | 2026-02-02 |
plot_K9_family(LTR_K27ac_H3K9me3_lfc,"H3K9me3","LTR","LTR")+
scale_color_manual(values = cluster_colors, drop = FALSE)
| Version | Author | Date |
|---|---|---|
| dc70156 | reneeisnowhere | 2026-02-02 |
sessionInfo()R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] smplot2_0.2.5 ggVennDiagram_1.5.4 ChIPseeker_1.42.1
[4] DT_0.33 ggrepel_0.9.6 rtracklayer_1.66.0
[7] genomation_1.38.0 plyranges_1.26.0 GenomicRanges_1.58.0
[10] GenomeInfoDb_1.42.3 IRanges_2.40.1 S4Vectors_0.44.0
[13] BiocGenerics_0.52.0 lubridate_1.9.4 forcats_1.0.0
[16] stringr_1.5.1 dplyr_1.1.4 purrr_1.1.0
[19] readr_2.1.5 tidyr_1.3.1 tibble_3.3.0
[22] ggplot2_3.5.2 tidyverse_2.0.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] splines_4.4.2
[2] later_1.4.2
[3] BiocIO_1.16.0
[4] bitops_1.0-9
[5] ggplotify_0.1.2
[6] R.oo_1.27.1
[7] XML_3.99-0.18
[8] rpart_4.1.24
[9] lifecycle_1.0.4
[10] rstatix_0.7.2
[11] rprojroot_2.1.1
[12] vroom_1.6.5
[13] processx_3.8.6
[14] lattice_0.22-7
[15] crosstalk_1.2.2
[16] backports_1.5.0
[17] magrittr_2.0.3
[18] Hmisc_5.2-3
[19] sass_0.4.10
[20] rmarkdown_2.29
[21] jquerylib_0.1.4
[22] yaml_2.3.10
[23] plotrix_3.8-4
[24] httpuv_1.6.16
[25] ggtangle_0.0.7
[26] cowplot_1.2.0
[27] DBI_1.2.3
[28] RColorBrewer_1.1-3
[29] abind_1.4-8
[30] zlibbioc_1.52.0
[31] R.utils_2.13.0
[32] RCurl_1.98-1.17
[33] yulab.utils_0.2.1
[34] nnet_7.3-20
[35] rappdirs_0.3.3
[36] git2r_0.36.2
[37] GenomeInfoDbData_1.2.13
[38] enrichplot_1.26.6
[39] tidytree_0.4.6
[40] codetools_0.2-20
[41] DelayedArray_0.32.0
[42] DOSE_4.0.1
[43] tidyselect_1.2.1
[44] aplot_0.2.8
[45] UCSC.utils_1.2.0
[46] farver_2.1.2
[47] matrixStats_1.5.0
[48] base64enc_0.1-3
[49] GenomicAlignments_1.42.0
[50] jsonlite_2.0.0
[51] Formula_1.2-5
[52] tools_4.4.2
[53] treeio_1.30.0
[54] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[55] Rcpp_1.1.0
[56] glue_1.8.0
[57] gridExtra_2.3
[58] SparseArray_1.6.2
[59] xfun_0.52
[60] qvalue_2.38.0
[61] MatrixGenerics_1.18.1
[62] withr_3.0.2
[63] fastmap_1.2.0
[64] boot_1.3-32
[65] callr_3.7.6
[66] caTools_1.18.3
[67] digest_0.6.37
[68] timechange_0.3.0
[69] R6_2.6.1
[70] gridGraphics_0.5-1
[71] seqPattern_1.38.0
[72] colorspace_2.1-1
[73] GO.db_3.20.0
[74] gtools_3.9.5
[75] dichromat_2.0-0.1
[76] RSQLite_2.4.3
[77] R.methodsS3_1.8.2
[78] utf8_1.2.6
[79] generics_0.1.4
[80] data.table_1.17.8
[81] httr_1.4.7
[82] htmlwidgets_1.6.4
[83] S4Arrays_1.6.0
[84] whisker_0.4.1
[85] pkgconfig_2.0.3
[86] gtable_0.3.6
[87] blob_1.2.4
[88] impute_1.80.0
[89] XVector_0.46.0
[90] htmltools_0.5.8.1
[91] carData_3.0-5
[92] pwr_1.3-0
[93] fgsea_1.32.4
[94] scales_1.4.0
[95] Biobase_2.66.0
[96] png_0.1-8
[97] ggfun_0.2.0
[98] knitr_1.50
[99] rstudioapi_0.17.1
[100] tzdb_0.5.0
[101] reshape2_1.4.4
[102] rjson_0.2.23
[103] checkmate_2.3.3
[104] nlme_3.1-168
[105] curl_7.0.0
[106] zoo_1.8-14
[107] cachem_1.1.0
[108] KernSmooth_2.23-26
[109] parallel_4.4.2
[110] foreign_0.8-90
[111] AnnotationDbi_1.68.0
[112] restfulr_0.0.16
[113] pillar_1.11.0
[114] vctrs_0.6.5
[115] gplots_3.2.0
[116] ggpubr_0.6.1
[117] promises_1.3.3
[118] car_3.1-3
[119] cluster_2.1.8.1
[120] htmlTable_2.4.3
[121] evaluate_1.0.5
[122] GenomicFeatures_1.58.0
[123] cli_3.6.5
[124] compiler_4.4.2
[125] Rsamtools_2.22.0
[126] rlang_1.1.6
[127] crayon_1.5.3
[128] ggsignif_0.6.4
[129] labeling_0.4.3
[130] ps_1.9.1
[131] getPass_0.2-4
[132] plyr_1.8.9
[133] fs_1.6.6
[134] stringi_1.8.7
[135] gridBase_0.4-7
[136] BiocParallel_1.40.2
[137] Biostrings_2.74.1
[138] lazyeval_0.2.2
[139] GOSemSim_2.32.0
[140] Matrix_1.7-3
[141] BSgenome_1.74.0
[142] hms_1.1.3
[143] patchwork_1.3.2
[144] bit64_4.6.0-1
[145] KEGGREST_1.46.0
[146] SummarizedExperiment_1.36.0
[147] broom_1.0.9
[148] igraph_2.1.4
[149] memoise_2.0.1
[150] bslib_0.9.0
[151] ggtree_3.14.0
[152] fastmatch_1.1-6
[153] bit_4.6.0
[154] ape_5.8-1