CountQC

Settings

	Setting
Reference:	Sparus_aurata/Ensembl/fSpaAur1.1/Annotation/Release_113-2025-01-13
Normalization method:	logMean
Log2 signal threshold:	3.322
Linear signal threshold:	10
Feature level:	gene
Number of features:	24752
Data Column Used:	matchCounts

Live Report and Visualizations

2025-02-07 13:52:32

Data Files

The data files are in tabular text format and can also be opened with a spreadsheet program (e.g. Excel).

When opening with Excel, do make sure that the Gene symbols are loaded into a column formatted as ‘text’ that prevents conversion of the symbols to dates). See

(https://www.genenames.org/help/importing-gene-symbol-data-into-excel-correctly)

Count_QC-raw-count.xlsx

Count_QC-normalized-signal.xlsx

Count_QC-rpkm.xlsx

Count_QC-tpm.xlsx

Count_QC-normalized-signal-viewHighExpressionGenes.html

Count Statistics

Correlation/Clustering Plot

Sample correlation

Clustering of High Variance Features

Threshold for std. dev. of log2 signal across samples: 0.508

Number of features with high std. dev.: 2000

GO categories of feature clusters

	BP	MF	CC
Cluster 1	Cluster-BP-1.html	Cluster-MF-1.html
Cluster 2	Cluster-BP-2.html	Cluster-MF-2.html	Cluster-CC-2.html
Cluster 3	Cluster-BP-3.html	Cluster-MF-3.html
Cluster 4	Cluster-BP-4.html	Cluster-MF-4.html
Cluster 5	Cluster-BP-5.html	Cluster-MF-5.html
Cluster 6	Cluster-BP-6.html	Cluster-MF-6.html	Cluster-CC-6.html
Note:
Cluster font color corresponds to the row colors in the heatmap plot.

GO cluster tables

Heatmap cluster members

Evaluate number of gene clusters

Multiple metrics were computed for a comprehensive assessment.

• Compactness: Dunn Index, CH Index
• Separation: Silhouette Width,Davies-Bouldin Index
• Cluster Stability: Gap Statistic, Entropy

MDS Plot

Scatter Plots by Conditions

allPairs

condition SDY

condition Control

Input Dataset

SessionInfo

## [1] "2025-02-07 13:55:05"

## ezRun tag: ed29b51d935a7281b59ff7ca5e23d187e8f449d3 
## ezRun github link: https://github.com/uzh/ezRun/tree/ed29b51d935a7281b59ff7ca5e23d187e8f449d3 
##  
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Debian GNU/Linux 12 (bookworm)
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Europe/Zurich
## tzcode source: system (glibc)
## 
## attached base packages:
##  [1] parallel  tools     stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] ggrepel_0.9.6               htmlwidgets_1.6.4          
##  [3] edgeR_4.4.1                 limma_3.62.1               
##  [5] GO.db_3.20.0                annotate_1.84.0            
##  [7] XML_3.99-0.17               GOstats_2.72.0             
##  [9] graph_1.84.0                Category_2.72.0            
## [11] AnnotationDbi_1.68.0        pheatmap_1.0.12            
## [13] SingleCellExperiment_1.28.1 Matrix_1.7-1               
## [15] htmltools_0.5.8.1           DT_0.33                    
## [17] RColorBrewer_1.1-3          clusterSim_0.51-5          
## [19] MASS_7.3-61                 fpc_2.2-13                 
## [21] cluster_2.1.8               ggpubr_0.6.0               
## [23] cowplot_1.1.3               gridExtra_2.3              
## [25] writexl_1.5.1               reshape2_1.4.4             
## [27] plotly_4.10.4               WGCNA_1.73                 
## [29] fastcluster_1.2.6           dynamicTreeCut_1.63-1      
## [31] kableExtra_1.4.0            knitr_1.49                 
## [33] qs2_0.1.4                   rtracklayer_1.66.0         
## [35] SummarizedExperiment_1.36.0 Biobase_2.66.0             
## [37] MatrixGenerics_1.18.0       matrixStats_1.4.1          
## [39] ezRun_3.20.1                lubridate_1.9.4            
## [41] forcats_1.0.0               stringr_1.5.1              
## [43] dplyr_1.1.4                 purrr_1.0.2                
## [45] readr_2.1.5                 tidyr_1.3.1                
## [47] tibble_3.2.1                ggplot2_3.5.1              
## [49] tidyverse_2.0.0             GenomicRanges_1.58.0       
## [51] Biostrings_2.74.0           GenomeInfoDb_1.42.1        
## [53] XVector_0.46.0              IRanges_2.40.1             
## [55] S4Vectors_0.44.0            BiocGenerics_0.52.0        
## [57] data.table_1.16.4          
## 
## loaded via a namespace (and not attached):
##   [1] splines_4.4.2            BiocIO_1.16.0            filelock_1.0.3          
##   [4] bitops_1.0-9             BiasedUrn_2.0.12         preprocessCore_1.69.0   
##   [7] rpart_4.1.23             httr2_1.0.7              lifecycle_1.0.4         
##  [10] rstatix_0.7.2            doParallel_1.0.17        lattice_0.22-6          
##  [13] vroom_1.6.5              prabclus_2.3-4           crosstalk_1.2.1         
##  [16] backports_1.5.0          magrittr_2.0.3           Hmisc_5.2-1             
##  [19] sass_0.4.9               rmarkdown_2.29           jquerylib_0.1.4         
##  [22] yaml_2.3.10              flexmix_2.3-19           DBI_1.2.3               
##  [25] ade4_1.7-22              abind_1.4-8              zlibbioc_1.52.0         
##  [28] RCurl_1.98-1.16          nnet_7.3-19              rappdirs_0.3.3          
##  [31] GenomeInfoDbData_1.2.13  AnnotationForge_1.48.0   genefilter_1.88.0       
##  [34] svglite_2.1.3            codetools_0.2-20         DelayedArray_0.32.0     
##  [37] xml2_1.3.6               tidyselect_1.2.1         farver_2.1.2            
##  [40] UCSC.utils_1.2.0         goseq_1.58.0             BiocFileCache_2.14.0    
##  [43] base64enc_0.1-3          GenomicAlignments_1.42.0 jsonlite_1.8.9          
##  [46] e1071_1.7-16             Formula_1.2-5            survival_3.7-0          
##  [49] iterators_1.0.14         systemfonts_1.1.0        foreach_1.5.2           
##  [52] progress_1.2.3           Rcpp_1.0.13.6            glue_1.8.0              
##  [55] SparseArray_1.6.0        mgcv_1.9-1               geneLenDataBase_1.42.0  
##  [58] xfun_0.49                withr_3.0.2              fastmap_1.2.0           
##  [61] digest_0.6.37            timechange_0.3.0         R6_2.5.1                
##  [64] colorspace_2.1-1         biomaRt_2.62.0           RSQLite_2.3.9           
##  [67] diptest_0.77-1           generics_0.1.3           robustbase_0.99-4-1     
##  [70] class_7.3-22             prettyunits_1.2.0        httr_1.4.7              
##  [73] S4Arrays_1.6.0           pkgconfig_2.0.3          gtable_0.3.6            
##  [76] modeltools_0.2-23        blob_1.2.4               impute_1.80.0           
##  [79] carData_3.0-5            RBGL_1.82.0              GSEABase_1.68.0         
##  [82] scales_1.3.0             png_0.1-8                rstudioapi_0.17.1       
##  [85] tzdb_0.4.0               rjson_0.2.23             nlme_3.1-166            
##  [88] checkmate_2.3.2          curl_6.0.1               proxy_0.4-27            
##  [91] cachem_1.1.0             foreign_0.8-87           restfulr_0.0.15         
##  [94] pillar_1.10.0            grid_4.4.2               vctrs_0.6.5             
##  [97] stringfish_0.16.0        car_3.1-3                dbplyr_2.5.0            
## [100] xtable_1.8-4             htmlTable_2.4.3          Rgraphviz_2.50.0        
## [103] evaluate_1.0.1           GenomicFeatures_1.58.0   locfit_1.5-9.10         
## [106] cli_3.6.3                compiler_4.4.2           Rsamtools_2.22.0        
## [109] rlang_1.1.4              crayon_1.5.3             ggsignif_0.6.4          
## [112] mclust_6.1.1             plyr_1.8.9               stringi_1.8.4           
## [115] viridisLite_0.4.2        BiocParallel_1.40.0      txdbmaker_1.2.1         
## [118] munsell_0.5.1            lazyeval_0.2.2           hms_1.1.3               
## [121] bit64_4.5.2              statmod_1.5.0            KEGGREST_1.46.0         
## [124] kernlab_0.9-33           broom_1.0.7              memoise_2.0.1           
## [127] RcppParallel_5.1.9       bslib_0.8.0              DEoptimR_1.1-3-1        
## [130] bit_4.5.0.1