CountQC

Settings

2025-11-25 16:09:30

	Setting
Reference:	Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03
Normalization method:	logMean
Log2 signal threshold:	3.322
Linear signal threshold:	10
Feature level:	gene
Number of features:	21077
Data Column Used:	matchCounts

Live Report and Visualizations

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: 0.5

Number of features with high std. dev.: 465

GO categories of feature clusters

	BP	MF	CC	Enrichr
Cluster 1	Cluster-BP-1.html		Cluster-CC-1.html	Enrichr
Cluster 2	Cluster-BP-2.html	Cluster-MF-2.html	Cluster-CC-2.html	Enrichr
Cluster 3	Cluster-BP-3.html	Cluster-MF-3.html	Cluster-CC-3.html	Enrichr
Cluster 4	Cluster-BP-4.html	Cluster-MF-4.html	Cluster-CC-4.html	Enrichr
Cluster 5	Cluster-BP-5.html	Cluster-MF-5.html	Cluster-CC-5.html	Enrichr
Cluster 6	Cluster-BP-6.html	Cluster-MF-6.html	Cluster-CC-6.html	Enrichr
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 undiff

Condition diff

EnrichR for topMarkers

Based on top 500 genes per sample selected by TPM and filtered for known housekeeping genes reported in the HRT atlas.

GeneSet enrichment

Sample	# of posMarkers	Enrichr link
AllSamples	446	Analyse at Enrichr website
S1_undiff	421	Analyse at Enrichr website
S2_undiff	427	Analyse at Enrichr website
S3_undiff	426	Analyse at Enrichr website
S4_diff	448	Analyse at Enrichr website
S5_diff	443	Analyse at Enrichr website
S6_diff	448	Analyse at Enrichr website

Input Dataset

SessionInfo

## [1] "2025-11-25 16:13:33"

## ezRun tag: 28496712ee737d3a120e054f95c1bc9b6b30a722 
## ezRun github link: https://github.com/uzh/ezRun/tree/28496712ee737d3a120e054f95c1bc9b6b30a722 
##  
## R version 4.5.0 (2025-04-11)
## 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  LAPACK version 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] htmlwidgets_1.6.4           edgeR_4.6.3                
##  [3] limma_3.64.3                GO.db_3.21.0               
##  [5] annotate_1.86.0             XML_3.99-0.18              
##  [7] GOstats_2.74.0              graph_1.86.0               
##  [9] Category_2.74.0             AnnotationDbi_1.70.0       
## [11] pheatmap_1.0.13             SingleCellExperiment_1.30.1
## [13] Matrix_1.7-3                htmltools_0.5.8.1          
## [15] DT_0.33                     RColorBrewer_1.1-3         
## [17] ggrepel_0.9.6               clusterSim_0.51-5          
## [19] MASS_7.3-65                 fpc_2.2-13                 
## [21] cluster_2.1.8.1             ggpubr_0.6.0               
## [23] cowplot_1.2.0               gridExtra_2.3              
## [25] writexl_1.5.4               reshape2_1.4.4             
## [27] plotly_4.11.0               WGCNA_1.73                 
## [29] fastcluster_1.3.0           dynamicTreeCut_1.63-1      
## [31] kableExtra_1.4.0            knitr_1.50                 
## [33] qs2_0.1.5                   rtracklayer_1.68.0         
## [35] SummarizedExperiment_1.38.1 Biobase_2.68.0             
## [37] MatrixGenerics_1.20.0       matrixStats_1.5.0          
## [39] ezRun_3.21.1                lubridate_1.9.4            
## [41] forcats_1.0.1               stringr_1.5.2              
## [43] dplyr_1.1.4                 purrr_1.1.0                
## [45] readr_2.1.5                 tidyr_1.3.1                
## [47] tibble_3.3.0                ggplot2_4.0.0              
## [49] tidyverse_2.0.0             GenomicRanges_1.60.0       
## [51] Biostrings_2.76.0           GenomeInfoDb_1.44.3        
## [53] XVector_0.48.0              IRanges_2.42.0             
## [55] S4Vectors_0.46.0            BiocGenerics_0.54.1        
## [57] generics_0.1.4              data.table_1.17.8          
## 
## loaded via a namespace (and not attached):
##   [1] splines_4.5.0            BiocIO_1.18.0            filelock_1.0.3          
##   [4] bitops_1.0-9             BiasedUrn_2.0.12         preprocessCore_1.70.0   
##   [7] rpart_4.1.24             httr2_1.1.2              lifecycle_1.0.4         
##  [10] rstatix_0.7.2            doParallel_1.0.17        lattice_0.22-7          
##  [13] vroom_1.6.5              prabclus_2.3-4           crosstalk_1.2.1         
##  [16] backports_1.5.0          magrittr_2.0.4           Hmisc_5.2-3             
##  [19] sass_0.4.10              rmarkdown_2.29           jquerylib_0.1.4         
##  [22] yaml_2.3.10              flexmix_2.3-20           DBI_1.2.3               
##  [25] ade4_1.7-23              abind_1.4-8              RCurl_1.98-1.17         
##  [28] nnet_7.3-20              rappdirs_0.3.3           GenomeInfoDbData_1.2.14 
##  [31] AnnotationForge_1.50.0   genefilter_1.90.0        svglite_2.2.1           
##  [34] codetools_0.2-20         DelayedArray_0.34.1      xml2_1.3.8              
##  [37] tidyselect_1.2.1         UCSC.utils_1.4.0         farver_2.1.2            
##  [40] goseq_1.60.0             BiocFileCache_2.16.0     base64enc_0.1-3         
##  [43] GenomicAlignments_1.44.0 jsonlite_2.0.0           e1071_1.7-16            
##  [46] Formula_1.2-5            survival_3.8-3           iterators_1.0.14        
##  [49] systemfonts_1.2.3        foreach_1.5.2            progress_1.2.3          
##  [52] Rcpp_1.1.0               glue_1.8.0               SparseArray_1.8.1       
##  [55] mgcv_1.9-3               geneLenDataBase_1.44.0   xfun_0.52               
##  [58] withr_3.0.2              fastmap_1.2.0            digest_0.6.37           
##  [61] timechange_0.3.0         R6_2.6.1                 textshaping_1.0.1       
##  [64] colorspace_2.1-1         biomaRt_2.64.0           dichromat_2.0-0.1       
##  [67] RSQLite_2.3.11           diptest_0.77-1           robustbase_0.99-4-1     
##  [70] class_7.3-23             prettyunits_1.2.0        httr_1.4.7              
##  [73] S4Arrays_1.8.1           pkgconfig_2.0.3          gtable_0.3.6            
##  [76] modeltools_0.2-24        blob_1.2.4               S7_0.2.0                
##  [79] impute_1.82.0            carData_3.0-5            RBGL_1.84.0             
##  [82] GSEABase_1.70.0          scales_1.4.0             png_0.1-8               
##  [85] rstudioapi_0.17.1        tzdb_0.5.0               rjson_0.2.23            
##  [88] nlme_3.1-168             checkmate_2.3.2          curl_6.2.3              
##  [91] proxy_0.4-27             cachem_1.1.0             foreign_0.8-90          
##  [94] restfulr_0.0.15          pillar_1.11.1            grid_4.5.0              
##  [97] vctrs_0.6.5              stringfish_0.16.0        car_3.1-3               
## [100] dbplyr_2.5.0             xtable_1.8-4             htmlTable_2.4.3         
## [103] Rgraphviz_2.52.0         evaluate_1.0.3           GenomicFeatures_1.60.0  
## [106] locfit_1.5-9.12          cli_3.6.5                compiler_4.5.0          
## [109] Rsamtools_2.24.0         rlang_1.1.6              crayon_1.5.3            
## [112] ggsignif_0.6.4           labeling_0.4.3           mclust_6.1.1            
## [115] plyr_1.8.9               stringi_1.8.7            viridisLite_0.4.2       
## [118] BiocParallel_1.42.2      txdbmaker_1.4.1          lazyeval_0.2.2          
## [121] hms_1.1.3                bit64_4.6.0-1            statmod_1.5.1           
## [124] KEGGREST_1.48.0          kernlab_0.9-33           broom_1.0.8             
## [127] memoise_2.0.1            RcppParallel_5.1.11-1    bslib_0.9.0             
## [130] DEoptimR_1.1-3-1         bit_4.6.0