1 Samples’ metadata

Reference paper: Conine et al., 2018.

Run Assay Type AvgSpotLen Bases BioProject BioSample Bytes Center Name Consent DATASTORE filetype DATASTORE provider DATASTORE region deveopmental_stage Experiment GEO_Accession (exp) Instrument LibraryLayout LibrarySelection LibrarySource Organism Platform ReleaseDate rna_injected Sample Name source_name sperm_source SRA Study strain
SRR6838709 RNA-Seq 73 410911057 PRJNA438441 SAMN08716181 194361550 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794574 GSM3042079 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042079 cauda18 cauda SRP135754 FVB
SRR6838711 RNA-Seq 73 421487122 PRJNA438441 SAMN08715807 199023811 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794576 GSM3042081 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042081 cauda18 cauda SRP135754 FVB
SRR6838713 RNA-Seq 73 435631082 PRJNA438441 SAMN08715805 205452048 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794578 GSM3042083 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042083 cauda18 cauda SRP135754 FVB
SRR6838715 RNA-Seq 73 336261841 PRJNA438441 SAMN08715803 158282912 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794580 GSM3042085 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042085 cauda18 cauda SRP135754 FVB
SRR6838717 RNA-Seq 73 355272714 PRJNA438441 SAMN08715801 167136620 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794582 GSM3042087 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042087 cauda18 cauda SRP135754 FVB
SRR6838719 RNA-Seq 73 437911331 PRJNA438441 SAMN08715799 206188528 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794584 GSM3042089 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042089 cauda18 cauda SRP135754 FVB
SRR6838721 RNA-Seq 73 487569138 PRJNA438441 SAMN08715797 229408296 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794586 GSM3042091 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042091 cauda18 cauda SRP135754 FVB
SRR6838724 RNA-Seq 73 521324559 PRJNA438441 SAMN08715794 244837382 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794589 GSM3042094 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042094 cauda18 cauda SRP135754 FVB
SRR6838725 RNA-Seq 73 404854043 PRJNA438441 SAMN08715793 189754022 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794590 GSM3042095 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042095 cauda18 cauda SRP135754 FVB
SRR6838727 RNA-Seq 73 486923480 PRJNA438441 SAMN08715791 228456025 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794592 GSM3042097 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042097 cauda18 cauda SRP135754 FVB
SRR6838728 RNA-Seq 73 338874427 PRJNA438441 SAMN08715790 159758442 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794593 GSM3042098 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042098 cauda18 cauda SRP135754 FVB
SRR6838730 RNA-Seq 73 317036240 PRJNA438441 SAMN08715788 149122612 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794595 GSM3042100 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042100 cauda18 cauda SRP135754 FVB
SRR6838732 RNA-Seq 73 379892545 PRJNA438441 SAMN08715786 178965353 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794597 GSM3042102 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042102 cauda18 cauda SRP135754 FVB
SRR6838741 RNA-Seq 73 171312991 PRJNA438441 SAMN08716113 80565570 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794606 GSM3042111 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042111 cauda28 cauda SRP135754 FVB
SRR6838742 RNA-Seq 73 415766020 PRJNA438441 SAMN08716112 195488370 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794607 GSM3042112 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042112 cauda28 cauda SRP135754 FVB
SRR6838743 RNA-Seq 73 413091275 PRJNA438441 SAMN08715779 193612599 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794608 GSM3042113 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042113 cauda28 cauda SRP135754 FVB
SRR6838744 RNA-Seq 73 369837803 PRJNA438441 SAMN08716056 175482725 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794609 GSM3042114 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042114 cauda28 cauda SRP135754 FVB
SRR6838745 RNA-Seq 73 477722843 PRJNA438441 SAMN08716055 223725545 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794610 GSM3042115 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042115 cauda28 cauda SRP135754 FVB
SRR6838746 RNA-Seq 73 285995137 PRJNA438441 SAMN08716111 134611781 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794611 GSM3042116 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042116 cauda28 cauda SRP135754 FVB
SRR6838747 RNA-Seq 73 458996745 PRJNA438441 SAMN08716110 216224953 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794612 GSM3042117 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042117 cauda28 cauda SRP135754 FVB
SRR6838748 RNA-Seq 73 437404278 PRJNA438441 SAMN08716109 205306427 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794613 GSM3042118 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042118 cauda28 cauda SRP135754 FVB
SRR6838749 RNA-Seq 73 432663281 PRJNA438441 SAMN08716108 203605454 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794614 GSM3042119 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042119 cauda28 cauda SRP135754 FVB
SRR6838750 RNA-Seq 73 271430850 PRJNA438441 SAMN08716107 127569874 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794615 GSM3042120 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042120 cauda28 cauda SRP135754 FVB
SRR6838751 RNA-Seq 73 289056462 PRJNA438441 SAMN08716106 135326595 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794616 GSM3042121 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042121 cauda28 cauda SRP135754 FVB
SRR6838752 RNA-Seq 73 198157052 PRJNA438441 SAMN08716105 93120934 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794617 GSM3042122 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042122 cauda28 cauda SRP135754 FVB
SRR6838753 RNA-Seq 73 379306525 PRJNA438441 SAMN08716104 177866539 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794618 GSM3042123 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042123 cauda28 cauda SRP135754 FVB
SRR6838758 RNA-Seq 73 359503656 PRJNA438441 SAMN08716099 168732505 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794623 GSM3042128 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042128 cauda28 cauda SRP135754 FVB
SRR6838759 RNA-Seq 73 332979760 PRJNA438441 SAMN08716098 156165846 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794624 GSM3042129 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042129 cauda28 cauda SRP135754 FVB
SRR6838760 RNA-Seq 73 396840227 PRJNA438441 SAMN08716097 186076297 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794625 GSM3042130 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042130 cauda28 cauda SRP135754 FVB
SRR6838761 RNA-Seq 73 397397399 PRJNA438441 SAMN08716096 185683658 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794626 GSM3042131 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042131 cauda28 cauda SRP135754 FVB
SRR6838762 RNA-Seq 73 445383724 PRJNA438441 SAMN08716095 208536585 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794627 GSM3042132 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042132 cauda28 cauda SRP135754 FVB
SRR6838763 RNA-Seq 73 423555424 PRJNA438441 SAMN08716094 197184040 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794628 GSM3042133 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042133 cauda28 cauda SRP135754 FVB
SRR6838764 RNA-Seq 73 546262484 PRJNA438441 SAMN08716093 256039773 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794629 GSM3042134 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042134 cauda28 cauda SRP135754 FVB
SRR6838708 RNA-Seq 73 386621690 PRJNA438441 SAMN08716182 182695051 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794573 GSM3042078 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042078 cauda18 cauda SRP135754 FVB
SRR6838710 RNA-Seq 73 388595867 PRJNA438441 SAMN08715809 183684132 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794575 GSM3042080 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042080 cauda18 cauda SRP135754 FVB
SRR6838712 RNA-Seq 73 482393873 PRJNA438441 SAMN08715806 227385131 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794577 GSM3042082 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042082 cauda18 cauda SRP135754 FVB
SRR6838714 RNA-Seq 73 455708936 PRJNA438441 SAMN08715804 214564522 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794579 GSM3042084 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042084 cauda18 cauda SRP135754 FVB
SRR6838716 RNA-Seq 73 352735416 PRJNA438441 SAMN08715802 166079963 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794581 GSM3042086 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042086 cauda18 cauda SRP135754 FVB
SRR6838718 RNA-Seq 73 625422599 PRJNA438441 SAMN08715800 293280874 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794583 GSM3042088 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042088 cauda18 cauda SRP135754 FVB
SRR6838720 RNA-Seq 73 391596405 PRJNA438441 SAMN08715798 184618859 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794585 GSM3042090 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042090 cauda18 cauda SRP135754 FVB
SRR6838722 RNA-Seq 73 428061271 PRJNA438441 SAMN08715796 201275999 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794587 GSM3042092 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042092 cauda18 cauda SRP135754 FVB
SRR6838723 RNA-Seq 73 444699930 PRJNA438441 SAMN08715795 208757571 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794588 GSM3042093 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042093 cauda18 cauda SRP135754 FVB
SRR6838726 RNA-Seq 73 544401254 PRJNA438441 SAMN08715792 255448276 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794591 GSM3042096 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042096 cauda18 cauda SRP135754 FVB
SRR6838729 RNA-Seq 73 379214940 PRJNA438441 SAMN08715789 178673985 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794594 GSM3042099 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042099 cauda18 cauda SRP135754 FVB
SRR6838731 RNA-Seq 73 301434415 PRJNA438441 SAMN08715787 141643256 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794596 GSM3042101 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042101 cauda18 cauda SRP135754 FVB
SRR6838754 RNA-Seq 73 365841045 PRJNA438441 SAMN08716103 171714554 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794619 GSM3042124 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042124 cauda28 cauda SRP135754 FVB
SRR6838755 RNA-Seq 73 508635871 PRJNA438441 SAMN08716102 237773684 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794620 GSM3042125 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042125 cauda28 cauda SRP135754 FVB
SRR6838756 RNA-Seq 73 354184734 PRJNA438441 SAMN08716101 167112344 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794621 GSM3042126 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042126 cauda28 cauda SRP135754 FVB
SRR6838757 RNA-Seq 73 292341123 PRJNA438441 SAMN08716100 139811179 GEO public fastq,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 2C embryo SRX3794622 GSM3042127 NextSeq 500 PAIRED cDNA TRANSCRIPTOMIC Mus musculus ILLUMINA 2018-07-26 none GSM3042127 cauda28 cauda SRP135754 FVB

2 Heatmap for quality assessment

After applying the log2(n + 1) transformation, I plot heatmap of normalized counts for top highly expressed genes to check for eventual big sample heterogeneity present in the dataset.

Sample SRX3794606 is an outlier of the 28h time point.

3 Finding Differentially Expressed Genes

3.1 DESeq2

3.2 Wilcoxon test, after edgeR normalization

I proceed as advised in Li et al. Genome Biology 2022 for big datasets (e.g. num samples ~ 100):

  1. edgeR normalization
  2. Wilcoxon non parametric statistical test.

3.3 Comparing the 2 methods with EGA genes

  • EGA genes are from Li et al. Nature 2018 and defined as RPKM oocyte < 0.5 and RPKM 2c > 2
  • “DESeq embr” and “edgeR wilcoxo embr” genes are DEGs found with the two methods with log2FC > 1 between the 18h and the 28h 2c
  • “DESeq mat” and “edgeR wilcoxo mat” genes are DEGs found with the two methods with log2FC < -1 between the 18h and the 28h 2c

Conclusion: DESeq does find more genes than Wilcoxon test after edgeR, but some of these additional genes are overlapping with EGA genes.

4 Defining strictly-EGA and strictly-maternal transcripts

I define:

sessionInfo()
## R version 4.1.3 (2022-03-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.6 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] gplots_3.1.3                readxl_1.4.1               
##  [3] edgeR_3.36.0                limma_3.50.3               
##  [5] dplyr_1.0.10                vsn_3.62.0                 
##  [7] ggrepel_0.9.2               pheatmap_1.0.12            
##  [9] gridExtra_2.3               ggpubr_0.5.0               
## [11] DESeq2_1.34.0               SummarizedExperiment_1.24.0
## [13] Biobase_2.54.0              MatrixGenerics_1.6.0       
## [15] matrixStats_0.62.0          GenomicRanges_1.46.1       
## [17] GenomeInfoDb_1.30.1         IRanges_2.28.0             
## [19] S4Vectors_0.32.4            BiocGenerics_0.40.0        
## [21] data.table_1.14.6           reshape2_1.4.4             
## [23] ggplot2_3.4.0              
## 
## loaded via a namespace (and not attached):
##  [1] colorspace_2.0-3       ggsignif_0.6.4         XVector_0.34.0        
##  [4] rstudioapi_0.14        farver_2.1.1           affyio_1.64.0         
##  [7] bit64_4.0.5            AnnotationDbi_1.56.2   fansi_1.0.3           
## [10] codetools_0.2-18       splines_4.1.3          cachem_1.0.6          
## [13] geneplotter_1.72.0     knitr_1.40             jsonlite_1.8.3        
## [16] broom_1.0.1            annotate_1.72.0        ashr_2.2-54           
## [19] png_0.1-7              BiocManager_1.30.22    compiler_4.1.3        
## [22] httr_1.4.4             backports_1.4.1        assertthat_0.2.1      
## [25] Matrix_1.5-3           fastmap_1.1.0          cli_3.4.1             
## [28] htmltools_0.5.3        tools_4.1.3            gtable_0.3.1          
## [31] glue_1.6.2             GenomeInfoDbData_1.2.7 affy_1.72.0           
## [34] Rcpp_1.0.9             carData_3.0-5          cellranger_1.1.0      
## [37] jquerylib_0.1.4        vctrs_0.5.1            Biostrings_2.62.0     
## [40] preprocessCore_1.56.0  xfun_0.35              stringr_1.4.1         
## [43] irlba_2.3.5.1          lifecycle_1.0.3        gtools_3.9.3          
## [46] rstatix_0.7.1          XML_3.99-0.12          zlibbioc_1.40.0       
## [49] scales_1.2.1           parallel_4.1.3         RColorBrewer_1.1-3    
## [52] yaml_2.3.6             memoise_2.0.1          sass_0.4.2            
## [55] stringi_1.7.8          RSQLite_2.2.18         SQUAREM_2021.1        
## [58] highr_0.9              genefilter_1.76.0      caTools_1.18.2        
## [61] BiocParallel_1.28.3    truncnorm_1.0-8        rlang_1.0.6           
## [64] pkgconfig_2.0.3        bitops_1.0-7           evaluate_0.18         
## [67] lattice_0.20-45        invgamma_1.1           purrr_0.3.5           
## [70] bit_4.0.5              tidyselect_1.2.0       plyr_1.8.8            
## [73] magrittr_2.0.3         R6_2.5.1               generics_0.1.3        
## [76] DelayedArray_0.20.0    DBI_1.1.3              pillar_1.8.1          
## [79] withr_2.5.0            prettydoc_0.4.1        mixsqp_0.3-48         
## [82] survival_3.2-13        KEGGREST_1.34.0        abind_1.4-5           
## [85] RCurl_1.98-1.9         tibble_3.1.8           crayon_1.5.2          
## [88] car_3.1-1              KernSmooth_2.23-20     utf8_1.2.2            
## [91] rmarkdown_2.18         locfit_1.5-9.6         grid_4.1.3            
## [94] blob_1.2.3             digest_0.6.30          xtable_1.8-4          
## [97] tidyr_1.2.1            munsell_0.5.0          bslib_0.4.1