miRTalk tutorial
Pre-processing
rev_gene()
Revise genes with rev_gene()
. For scRNA-seq data, we
suggest to revise the gene symbols with rev_gene()
.
geneinfo
is the system data.frame containing the
information of human and mouse from NCBI gene(updated in June. 19,
2022). To use your own geneinfo
data.frame, please refer to
demo_geneinfo()
to build a new one, e.g., rat, zebrafish,
Drosophila, C. elegans, etc.
Parameters of rev_gene()
see below:
data
A data.frame or matrix or dgCMatrixdata_type
A character to define the type ofdata
, select ‘count’ for the data matrix, ‘mir_info’ for the mir_info data.frame, ‘mir2tar’ for the mir2tar data.frame, ‘pathways’ for the pathways data.frame, ‘gene2go’ for the gene2go data.framespecies
Species of the data.’Human’, ‘Mouse’ or ‘Rat’geneinfo
A data.frame of the system data containing gene symbols of ‘Human’, ‘Mouse’ and ‘Rat’ updated on June 19, 2022 for revising gene symbols
library(miRTalk)
#> 载入需要的程辑包:doParallel
#> Warning: 程辑包'doParallel'是用R版本4.1.3 来建造的
#> 载入需要的程辑包:foreach
#> 载入需要的程辑包:iterators
#> 载入需要的程辑包:parallel
#> Warning: replacing previous import 'Seurat::JS' by 'networkD3::JS' when loading
#> 'miRTalk'
load(paste0(system.file(package = "miRTalk"), "/extdata/example.rda"))
# demo_geneinfo
demo_geneinfo()
#> symbol synonyms species
#> 1 A1BG A1B Human
#> 2 A1BG ABG Human
#> 3 A2MP1 A2MP Human
#> 4 Aco1 Aco Mouse
#> 5 Alb1 Alb Rat
# demo_sc_data
demo_sc_data()
#> 6 x 6 sparse Matrix of class "dgCMatrix"
#> cell1 cell2 cell3 cell4 cell5 cell6
#> A1BG 19 20 14 48 . 17
#> A2M . 3 45 . . 29
#> A2MP . 44 18 10 . .
#> NAT1 5 . . . . 35
#> NAT2 . . 7 . . .
#> NATP . . 44 45 . 32
# revise gene symbols
<- rev_gene(data = sc_data,data_type = "count",species = "Human",geneinfo = geneinfo) sc_data
Processing
create_miRTalk()
Create miRTalk object with create_miRTalk()
. Users need
to provide the raw count data and the cell type for
create_miRTalk()
. miRTalk will use
NormalizeData()
in Seurat
to normalize data by
default. If your data has been normalized by other methods, you can set
the parameter if_normalize = FALSE
Parameters of create_miRTalk()
see below:
sc_data
mA data.frame or matrix or dgCMatrix containing raw counts of single-cell RNA-seq datasc_celltype
A character containing the cell type of the single-cell RNA-seq dataspecies
A character meaning species of the single-cell transcriptomics data. “Human”, “Mouse”, “Rat”if_normalize
Normalize sc_data withSeurat
LogNormalize()
<- create_miRTalk(sc_data = sc_data, sc_celltype = sc_celltype, species = "Human")
obj
obj#> An object of class miRTalk
#> 0 EV-derived miRNA-target interactions
# If your data has been normalized by other methods, you can set the parameter `if_normalize = FALSE`
# obj <- create_miRTalk(sc_data = sc_data, sc_celltype = sc_celltype, species = "Human", if_normalize = FALSE)
find_miRNA()
Find expressed miRNAs among all cells with find_miRNA()
.
Users need to provided a EV-derived miRNA database for
find_miRNA()
. mir_info
is the system
data.frame containing information of EV-derived miRNA of “Human”,
“Mouse”, and “Rat”. To use your own mir_info data.frame, please refer to
demo_mir_info()
to build a new one, e.g., zebrafish,
Drosophila, C. elegans, etc.
Parameters of find_miRNA()
see below:
object
miRTalk object aftercreate_miRTalk()
mir_info
A data.frame of the system data containing information of EV-derived miRNA of “Human”, “Mouse”, and “Rat”
# demo_mir_info
demo_mir_info()
#> miRNA miRNA_mature gene species
#> 1 hsa-miR-1 hsa-miR-1-5p MIR1-1 Human
#> 2 hsa-miR-1 hsa-miR-1-5p MIR1-2 Human
#> 3 hsa-miR-1 hsa-miR-1-3p MIR1-1 Human
#> 4 hsa-miR-1 hsa-miR-1-3p MIR1-2 Human
#> 5 mmu-miR-105 mmu-miR-105 Mir105 Mouse
#> 6 rno-miR-106b rno-miR-106b-5p Mir106b Rat
# find highly expressed LR pairs
<- find_miRNA(object = obj, mir_info = mir_info) obj
find_hvtg()
Find highly variable target genes with DEGs and HVGs
find_hvtg()
. miRTalk uses the top 3000 HVGs and DEGs for
each cell types with Seurat
methods. The result is a
character stored obj@data$var_genes
. Users can use their
own methods to find Find highly variable target genes and replace
them
Parameters of find_hvtg()
see below:
object
miRTalk object aftercreate_miRTalk()
pvalue
Cutoff of p value. Default is 0.05log2fc
log2 fold change for identifying the highly expressed genes in each cell type. Default is 0.5min_cell_num
Min cell number for each cell type. Default is 10nfeatures
Number of features to select as top variable features. Default is 3000
# find highly variable target genes
<- find_hvtg(object = obj)
obj
# the result is a character
<- obj@data$var_genes
var_genes str(var_genes)
#> chr [1:3377] "MGP" "LUM" "DCD" "DCN" "IGKV2D-28" "IGKV3-11" "SPINK1" ...
# if your have your own result, you can replace them with the following code
# object@data$var_genes <- your_own_var_genes
find_miRTalk()
Infer cell-cell communications mediated by EV-derived miRNAs from
senders to receivers with find_miRTalk()
. miRTalk uses the
curated mir2tar
database containing EV-derived miRNA-target
interactions. To use your own mir2tar data.frame, please refer to
demo_mir2tar()
to build a new one, e.g., zebrafish,
Drosophila, C. elegans, etc. The result is a character stored
obj@cci
. Users can use get_miRTalk_cci()
to
get simple results of miRNA-target interactions.
Parameters of find_miRTalk()
see below:
object
miRTalk object afterfind_miRNA()
andfind_hvtg()
mir2tar
A data.frame of the system data containing relationship of miRNA and its target genes for “Human”, “Mouse”, “Rat”min_cell_num
Min cell number for each cell type and expressed miRNA. Default is 10pvalue
Cutoff of p value. Default is 0.05resolution
Correct to precursor or mature miRNAs. Use ‘precursor’ or ‘mature’. Default is ‘mature’min_percent
Min percent of expressed cells for target genes of miRNA. Default is 0.05if_doParallel
Use doParallel. Default is TRUEuse_n_cores
umber of CPU cores to use. Default is 4
# demo_mir2tar
demo_mir2tar()
#> miRNA miRNA_mature target_gene species
#> 1 hsa-miR-1 hsa-miR-1-5p BDNF Human
#> 2 hsa-miR-1 hsa-miR-1-3p RBM28 Human
#> 3 mmu-miR-105 mmu-miR-105 Abl2 Mouse
#> 4 rno-miR-106b rno-miR-106b-5p Mcl1 Rat
# infer cell-cell communications mediated by EV-derived miRNAs from senders to receivers
<- find_miRTalk(object = obj, mir2tar = mir2tar)
obj
obj#> An object of class miRTalk
#> 2185 EV-derived miRNA-target interactions
# the result is a data.frame
<- obj@cci
cci str(cci)
#> 'data.frame': 2185 obs. of 17 variables:
#> $ celltype_sender : chr "Bcell" "Bcell" "Bcell" "Bcell" ...
#> $ celltype_receiver : chr "Bcell" "Bcell" "Bcell" "Bcell" ...
#> $ miRNA : chr "hsa-miR-4426" "hsa-miR-29b-3p" "hsa-miR-29b-3p" "hsa-miR-29b-3p" ...
#> $ miR_gene : chr "MIR4426" "MIR29B1" "MIR29B1" "MIR29B1" ...
#> $ percent_sender : num 0.19 0.231 0.231 0.231 0.231 ...
#> $ percent_receiver : num 0.19 0.231 0.231 0.231 0.231 ...
#> $ miRNA_activity : num 0.429 0.481 0.481 0.481 0.481 ...
#> $ target_gene : chr "PPIC" "CLDN1" "EREG" "TGFB3" ...
#> $ target_gene_activity : num 5.81e-03 3.45e-04 1.03e-04 3.43e-04 4.85e-05 ...
#> $ target_gene_mean_exp : num 0.02822 0.001677 0.000501 0.001667 0.000235 ...
#> $ target_gene_mean_exp_other: num 0.187 0.1058 0.1496 0.1191 0.0943 ...
#> $ target_gene_percent : num 0.0964 0.0843 0.0964 0.0723 0.0843 ...
#> $ target_gene_percent_other : num 0.403 0.208 0.211 0.303 0.164 ...
#> $ pvalue : num 1.58e-08 2.63e-03 3.73e-03 1.85e-06 1.81e-02 ...
#> $ sig : chr "YES" "YES" "YES" "YES" ...
#> $ prob : num 0.469 0.466 0.466 0.466 0.466 ...
#> $ score : num 0.426 0.48 0.481 0.48 0.481 ...
# get simple results of miRNA-target interactions
<- get_miRTalk_cci(obj)
obj_cci str(obj_cci)
#> 'data.frame': 2083 obs. of 9 variables:
#> $ celltype_sender : chr "Bcell" "Bcell" "Bcell" "Bcell" ...
#> $ celltype_receiver : chr "Bcell" "Bcell" "Bcell" "Bcell" ...
#> $ miRNA : chr "hsa-miR-4426" "hsa-miR-29b-3p" "hsa-miR-29b-3p" "hsa-miR-29b-3p" ...
#> $ miR_gene : chr "MIR4426" "MIR29B1" "MIR29B1" "MIR29B1" ...
#> $ miRNA_activity : num 0.429 0.481 0.481 0.481 0.481 ...
#> $ target_gene : chr "PPIC" "CLDN1" "EREG" "TGFB3" ...
#> $ target_gene_activity: num 5.81e-03 3.45e-04 1.03e-04 3.43e-04 4.85e-05 ...
#> $ prob : num 0.469 0.466 0.466 0.466 0.466 ...
#> $ score : num 0.426 0.48 0.481 0.48 0.481 ...
Visualization
plot_miRTalk_chord()
Parameters of plot_miRTalk_chord()
see below:
object
miRTalk object afterfind_miRTalk()
celltype
which cell types to plot by order. Default is to plot all cell typescelltype_color
Colors for the cell types, whose length must be equal tocelltype
miRNA
which miRNAs to use. Default is to plot all inferred miRNAsedge_color
Colors for the edges from the sender cell type, whose length must be equal to celltypeedge_type
Types for the edges from the sender cell type. Default is “big.arrow”. “ellipse” for ellipse, “triangle” for triangle, “curved” for curved. Details seecirclize::chordDiagram()
show_type
which type of miRNAs to show, “number”, “activity”, or “score” for sum of inferred miRNAs number and activity, respectively, or “prob” for max probability. Default is “number”if_show_autocrine
Whether to show autocrine. Default is FALSEtext_size
Size of text labels. Default is 1.5y_scale
y_scale to adjust the text. Default is 0.1...
parameters pass tocirclize::chordDiagram()
, e.g.,link.arr.width
,link.arr.length
,link.arr.col
plot_miRTalk_chord(object = obj)
plot_miRTalk_circle()
Parameters of plot_miRTalk_circle()
see below:
object
miRTalk object afterfind_miRTalk()
celltype
which cell types to plot. Default is to plot all cell typesmiRNA
which miRNAs to use. Default is to plot all inferred miRNAscelltype_color
Colors for the cell types, whose length must be equal tocelltype
edge_color
Colors for the edges from the sender cell type, whose length must be equal tocelltype
edge_type
Types for the edges. “fan” by default, “link”, “hive”show_type
which type of miRNAs to show, “number”, “activity”, or “score” for sum of inferred miRNAs number and activity, respectively, or “prob” for max probability. Default is “number”if_show_autocrine
Whether to show autocrine. Default isFALSE
edge_alpha
Transparency of edge. Default is 0.5node_size
Size of node. Default is 10text_size
Size of text. Default is 5
plot_miRTalk_circle(object = obj)
plot_miRTalk_circle_simple()
To show one or more senders or receivers by retaining all cell
types, users can use plot_miRTalk_circle_simple()
for
plotting.
Parameters of plot_miRTalk_circle_simple()
see
below:
object
miRTalk object afterfind_miRTalk()
celltype
which cell types to plot. one or more cell typescelltype_dir
which direction to plot, “sender” or “receiver”. Default is as “sender”miRNA
which miRNAs to use. Default is to plot all inferred miRNAscelltype_color
Colors for the cell types, whose length must be equal tocelltype
edge_color
Colors for the edges from the sender cell type, whose length must be equal tocelltype
edge_type
Types for the edges. “fan” by default, “link”, “hive”show_type
which type of miRNAs to show, “number”, “activity”, or “score” for sum of inferred miRNAs number and activity, respectively, or “prob” for max probability. Default is “number”if_show_autocrine
Whether to show autocrine. Default isFALSE
edge_alpha
Transparency of edge. Default is 0.5node_size
Size of node. Default is 10text_size
Size of text. Default is 5
# as sender
plot_miRTalk_circle_simple(object = obj, celltype = "Tumor", celltype_dir = "sender")
# as receiver
plot_miRTalk_circle_simple(object = obj, celltype = "Tumor", celltype_dir = "reciver")
plot_miRTalk_heatmap()
Parameters of plot_miRTalk_heatmap()
see below:
object
miRTalk object afterfind_miRTalk()
celltype
which cell types to plot. Default is to plot all cell typesmiRNA
which miRNAs to use. Default is to plot all inferred miRNAsshow_type
which type of miRNAs to show, “number”, “activity”, or “score” for sum of inferred miRNAs number and activity, respectively, or “prob” for max probability. Default is “number”text_size
Size of text labels. Default is 10viridis_option
option inviridis::scale_color_viridis
, can be “A”, “B”, “C”, “D”, “E”, “F”, “G”, “H”. Default is “D”...
parameters pass toheatmaply::heatmaply
, e.g., grid_color, grid_width
plot_miRTalk_heatmap(object = obj)
plot_miRTalk_sankey()
Parameters of plot_miRTalk_sankey()
see below:
object
miRTalk object afterfind_miRTalk()
celltype
which cell types to plot by order. Default is to plot all cell typesmiRNA
which miRNAs to use. Default is to plot all inferred miRNAscelltype_color
Colors for the cell types, whose length must be equal tocelltype
edge_color
Colors for the edges from the sender cell type, whose length must be equal tocelltype
, Or use “NO” to cancel itshow_type
which type of miRNAs to show, “number”, “activity”, or “score” for sum of inferred miRNAs number and activity, respectively, or “prob” for max probability. Default is “number”if_show_autocrine
Whether to show autocrine. Default is FALSEedge_alpha
Transparency of edge. Default is 0.5node_size
Size of node. Default is 40text_size
Size of text. Default is 15node_pad
Size of node padding. Numeric essentially influences the width height. Default is 20...
parameters pass tonetworkD3::sankeyNetwork
plot_miRTalk_sankey(object = obj)
plot_miR_heatmap()
Parameters of plot_miR_heatmap()
see below:
object
miRTalk object afterfind_miRTalk()
celltype
which cell types to plot. Default is to plot all cell typesmiRNA
which miRNAs to plot. Default is to plot all inferred miRNAstext_size
Size of text labels. Default is 10if_horizontal
Whether to plot with the horizontal direction. Default isTRUE
viridis_option
option inviridis::scale_color_viridis
, can be “A”, “B”, “C”, “D”, “E”, “F”, “G”, “H”. Default is “D”....
parameters pass toheatmaply::heatmaply
, e.g., grid_color, grid_width
plot_miR_heatmap(object = obj)
plot_miR_bubble()
Parameters of plot_miR_bubble()
see below:
object
miRTalk object afterfind_miRTalk()
celltype
which cell types to plot. Default is to plot all cell typesmiRNA
which miRNAs to plot. Default is to plot all inferred miRNAsif_show_autocrine
Whether to show autocrine. Default isFALSE
if_horizontal
Whether to plot with the horizontal direction. Default isTRUE
viridis_option
option inviridis::scale_color_viridis
, can be “A”, “B”, “C”, “D”, “E”, “F”, “G”, “H”. Default is “D”.
plot_miR_bubble(object = obj)
plot_miR2tar_chord()
Parameters of plot_miR2tar_chord()
see below:
object
miRTalk object afterfind_miRTalk()
celltype_sender
Name of celltype_sender. One or more cell typescelltype_receiver
Name of celltype_receiver. One or more cell typescelltype_color
Colors for the celltype_sender nodes and celltype_receiver nodes, or use “NO” to make it simplemiRNA
which miRNAs to use. Default is to plot all inferred miRNAsedge_color
Colors for the edges from the sender cell typeedge_type
Types for the edges from the sender cell type. Default is “circle”, “big.arrow” for big arrow, “triangle” for triangle, “ellipse” for ellipse, “curved” for curved. Details seecirclize::chordDiagram
show_type
which type of miRNAs to show, “prob” or “score” for inferred miRNAs-target interactions. Default is “prob”text_size
Size of text labels. Default is 0.5y_scale
y_scale to adjust the text. Default is 1...
parameters pass tocirclize::chordDiagram
, e.g.,link.arr.width
,link.arr.length
,link.arr.col
plot_miR2tar_chord(obj, celltype_sender = "Tumor", celltype_receiver = "Stromal")
plot_miR2tar_circle()
Parameters of plot_miR2tar_circle()
see below:
object
miRTalk object afterfind_miRTalk()
celltype_sender
Name of celltype_sender. One or more cell typescelltype_receiver
Name of celltype_receiver. One or more cell typescelltype_color
Colors for the celltype_sender nodes and celltype_receiver nodes, or use “NO” to make it simplemiRNA
which miRNAs to use. Default is to plot all inferred miRNAsedge_color
Colors for the edges from the sender cell typetext_size
Size of text labels. Default is 3edge_width
y_scale to adjust the text. Default is 0.5
plot_miR2tar_circle(obj, celltype_sender = "Tumor", celltype_receiver = "Stromal")
plot_miR2tar_circle(obj, celltype_sender = "Tumor", celltype_receiver = "Stromal", celltype_color = "NO")
plot_miR2tar_heatmap()
Parameters of plot_miR2tar_heatmap()
see below:
object
miRTalk object afterfind_miRTalk()
celltype_sender
Name of celltype_sender. One or more cell typescelltype_receiver
Name of celltype_receiver. One or more cell typesmiRNA
which miRNAs to use. Default is to plot all inferred miRNAsshow_type
which type of miRNAs to show, “prob” or “score” for inferred miRNAs-target interactions. Default is “prob”text_size
Size of text labels. Default is 3if_horizontal
Whether to plot with the horizontal direction. Default isTRUE
viridis_option
option inviridis::scale_color_viridis
, can be “A”, “B”, “C”, “D”, “E”, “F”, “G”, “H”. Default is “D”....
parameters pass toheatmaply::heatmaply
, e.g., grid_color
plot_miR2tar_heatmap(obj, celltype_sender = "Tumor", celltype_receiver = "Stromal", grid_color = "black")
Note
To get pathways of target genes, use
get_pathways()
Parameters of get_pathways()
see below:
object
miRTalk object afterfind_miRTalk()
pathways
A data.frame of the system data containing gene-gene interactions and pathways from KEGG and Reactome for ‘Human’, ‘Mouse’ or ‘Rat’. seedemo_pathways()
# demo_pathways
demo_pathways()
#> src dest pathway species
#> 1 CDKN1A CDK2 p53 signaling pathway Human
#> 2 CDKN1A CDK4 p53 signaling pathway Human
#> 3 CDK2 TP53 p53 signaling pathway Human
#> 4 Akt1 Atf2 PI3K-Akt signaling pathway Mouse
#> 5 Tcirg1 Ppa1 Oxidative phosphorylation Rat
# get pathways
<- get_pathways(obj, pathways = pathways)
obj_pathways head(obj_pathways)
#> target_genes id pathway species
#> 330 ALDOA hsa:00010 Glycolysis / Gluconeogenesis Human
#> 331 ALDOA hsa:00010 Glycolysis / Gluconeogenesis Human
#> 332 ALDOA hsa:00010 Glycolysis / Gluconeogenesis Human
#> 333 ALDOA hsa:00010 Glycolysis / Gluconeogenesis Human
#> 335 ALDOA hsa:00010 Glycolysis / Gluconeogenesis Human
#> 337 ALDOA hsa:00010 Glycolysis / Gluconeogenesis Human
To get GO terms of target genes, use get_gene2go()
Parameters of get_gene2go()
see below:
object
miRTalk object afterfind_miRTalk()
gene2go
A data.frame of the system data containing GO terms for ‘Human’, ‘Mouse’ or ‘Rat’. seedemo_gene2go()
if_show_negative
Whether to show the results with negative regulation. Default is TRUE.
# demo_gene2go
demo_gene2go()
#> symbol GO_term species
#> 1 A1BG molecular_function Human
#> 2 A1BG extracellular region Human
#> 3 A1BG extracellular space Human
#> 4 Zzz3 DNA binding Mouse
#> 5 Zyx metal ion binding Rat
# get pathways
<- get_gene2go(obj, gene2go = gene2go)
obj_gene2go head(obj_gene2go)
#> symbol evidence qualifier
#> 2851 DNAJB6 IDA involved_in
#> 2854 DNAJB6 IEA involved_in
#> 2865 DNAJB6 IDA involved_in
#> 2866 DNAJB6 IMP involved_in
#> 6714 NME6 IBA involved_in
#> 6715 NME6 IDA involved_in
#> GO_term
#> 2851 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
#> 2854 negative regulation of transcription, DNA-templated
#> 2865 negative regulation of inclusion body assembly
#> 2866 negative regulation of inclusion body assembly
#> 6714 negative regulation of cell growth
#> 6715 negative regulation of cell growth
#> PubMed category species
#> 2851 11896048 Process Human
#> 2854 - Process Human
#> 2865 21231916 Process Human
#> 2866 20889486 Process Human
#> 6714 21873635 Process Human
#> 6715 10618642 Process Human
To plot the sparse expression of miRNA genes in scRNA-seq, you can
use the Nebulosa::plot_density()
Nebulosa::plot_density(object = obj_seurat, features = "MIR24-2")
sessionInfo()
#> R version 4.1.1 (2021-08-10)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 19045)
#>
#> Matrix products: default
#>
#> locale:
#> [1] LC_COLLATE=Chinese (Simplified)_China.936
#> [2] LC_CTYPE=Chinese (Simplified)_China.936
#> [3] LC_MONETARY=Chinese (Simplified)_China.936
#> [4] LC_NUMERIC=C
#> [5] LC_TIME=Chinese (Simplified)_China.936
#>
#> attached base packages:
#> [1] parallel stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] miRTalk_1.0 doParallel_1.0.17 iterators_1.0.13 foreach_1.5.1
#>
#> loaded via a namespace (and not attached):
#> [1] circlize_0.4.13 plyr_1.8.6 igraph_1.2.7
#> [4] lazyeval_0.2.2 sp_1.4-5 splines_4.1.1
#> [7] crosstalk_1.2.0 listenv_0.8.0 scattermore_0.7
#> [10] ggplot2_3.3.6 digest_0.6.28 ca_0.71.1
#> [13] htmltools_0.5.2 viridis_0.6.2 fansi_0.5.0
#> [16] magrittr_2.0.1 tensor_1.5 cluster_2.1.2
#> [19] ROCR_1.0-11 limma_3.50.0 globals_0.14.0
#> [22] graphlayouts_0.7.1 matrixStats_0.61.0 spatstat.sparse_3.0-0
#> [25] prettyunits_1.1.1 rmdformats_1.0.3 colorspace_2.0-2
#> [28] ggrepel_0.9.1 xfun_0.30 dplyr_1.0.7
#> [31] crayon_1.4.2 jsonlite_1.7.2 progressr_0.9.0
#> [34] spatstat.data_3.0-0 survival_3.2-11 zoo_1.8-9
#> [37] glue_1.4.2 polyclip_1.10-0 registry_0.5-1
#> [40] gtable_0.3.0 webshot_0.5.4 leiden_0.3.9
#> [43] future.apply_1.8.1 shape_1.4.6 abind_1.4-5
#> [46] scales_1.1.1 pheatmap_1.0.12 DBI_1.1.1
#> [49] miniUI_0.1.1.1 Rcpp_1.0.7 progress_1.2.2
#> [52] viridisLite_0.4.0 xtable_1.8-4 reticulate_1.22
#> [55] spatstat.core_2.3-0 datawizard_0.6.2 htmlwidgets_1.5.4
#> [58] httr_1.4.2 RColorBrewer_1.1-2 ellipsis_0.3.2
#> [61] Seurat_4.1.1 ica_1.0-2 pkgconfig_2.0.3
#> [64] farver_2.1.0 sass_0.4.0 uwot_0.1.10
#> [67] deldir_1.0-6 utf8_1.2.2 labeling_0.4.2
#> [70] tidyselect_1.1.1 rlang_0.4.12 reshape2_1.4.4
#> [73] later_1.3.0 munsell_0.5.0 tools_4.1.1
#> [76] generics_0.1.1 ggridges_0.5.3 evaluate_0.14
#> [79] stringr_1.4.0 fastmap_1.1.0 heatmaply_1.4.0
#> [82] yaml_2.2.1 goftest_1.2-3 knitr_1.36
#> [85] fitdistrplus_1.1-6 tidygraph_1.2.0 purrr_0.3.4
#> [88] RANN_2.6.1 dendextend_1.16.0 ggraph_2.0.5
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