CountQC

Settings

	Setting
Reference:	Homo_sapiens/GENCODE/GRCh38.p13/Annotation/Release_42-2023-01-30
Normalization method:	logMean
Log2 signal threshold:	3.322
Linear signal threshold:	10
Feature level:	gene
Number of features:	21057
Data Column Used:	matchCounts

Live Report and Visualizations

2024-04-26 16:26:33

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.: 746

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-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

MDS Plot

Scatter Plots by Conditions

allPairs

Condition undiff

Condition diff

Input Dataset

SessionInfo

## [1] "2024-04-26 16:29:29"

## ezRun tag: c374ec67050e41361e171788c4b5e55b055634c9 
## ezRun github link: https://github.com/uzh/ezRun/tree/c374ec67050e41361e171788c4b5e55b055634c9 
##  
## R version 4.3.2 (2023-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 10 (buster)
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so;  LAPACK version 3.8.0
## 
## 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_0.9.4               htmlwidgets_1.6.2          
##  [3] edgeR_4.0.1                 limma_3.58.1               
##  [5] GO.db_3.18.0                annotate_1.80.0            
##  [7] XML_3.99-0.15               GOstats_2.68.0             
##  [9] graph_1.80.0                Category_2.68.0            
## [11] AnnotationDbi_1.64.1        pheatmap_1.0.12            
## [13] SingleCellExperiment_1.24.0 Matrix_1.6-1.1             
## [15] htmltools_0.5.7             DT_0.30                    
## [17] RColorBrewer_1.1-3          ggpubr_0.6.0               
## [19] cowplot_1.1.1               gridExtra_2.3              
## [21] writexl_1.4.2               reshape2_1.4.4             
## [23] plotly_4.10.3               WGCNA_1.72-1               
## [25] fastcluster_1.2.3           dynamicTreeCut_1.63-1      
## [27] kableExtra_1.3.4            knitr_1.45                 
## [29] rtracklayer_1.62.0          SummarizedExperiment_1.32.0
## [31] Biobase_2.62.0              MatrixGenerics_1.14.0      
## [33] matrixStats_1.1.0           ezRun_3.18.1               
## [35] lubridate_1.9.3             forcats_1.0.0              
## [37] stringr_1.5.1               dplyr_1.1.4                
## [39] purrr_1.0.2                 readr_2.1.4                
## [41] tidyr_1.3.0                 tibble_3.2.1               
## [43] ggplot2_3.5.0               tidyverse_2.0.0            
## [45] GenomicRanges_1.54.1        Biostrings_2.70.1          
## [47] GenomeInfoDb_1.38.1         XVector_0.42.0             
## [49] IRanges_2.36.0              S4Vectors_0.40.2           
## [51] BiocGenerics_0.48.1         data.table_1.14.8          
## 
## loaded via a namespace (and not attached):
##   [1] splines_4.3.2            BiocIO_1.12.0            filelock_1.0.2          
##   [4] bitops_1.0-7             BiasedUrn_2.0.11         preprocessCore_1.64.0   
##   [7] rpart_4.1.21             lifecycle_1.0.4          rstatix_0.7.2           
##  [10] doParallel_1.0.17        lattice_0.22-5           vroom_1.6.4             
##  [13] crosstalk_1.2.0          backports_1.4.1          magrittr_2.0.3          
##  [16] Hmisc_5.1-1              sass_0.4.7               rmarkdown_2.25          
##  [19] jquerylib_0.1.4          yaml_2.3.7               DBI_1.1.3               
##  [22] abind_1.4-5              zlibbioc_1.48.0          rvest_1.0.3             
##  [25] RCurl_1.98-1.13          nnet_7.3-19              rappdirs_0.3.3          
##  [28] GenomeInfoDbData_1.2.11  AnnotationForge_1.44.0   genefilter_1.84.0       
##  [31] svglite_2.1.2            codetools_0.2-19         DelayedArray_0.28.0     
##  [34] xml2_1.3.5               tidyselect_1.2.0         farver_2.1.1            
##  [37] goseq_1.54.0             BiocFileCache_2.10.1     base64enc_0.1-3         
##  [40] webshot_0.5.5            GenomicAlignments_1.38.0 jsonlite_1.8.7          
##  [43] ellipsis_0.3.2           Formula_1.2-5            survival_3.5-7          
##  [46] iterators_1.0.14         systemfonts_1.0.5        foreach_1.5.2           
##  [49] progress_1.2.2           Rcpp_1.0.11              glue_1.6.2              
##  [52] SparseArray_1.2.2        geneLenDataBase_1.38.0   mgcv_1.9-0              
##  [55] xfun_0.41                withr_2.5.2              fastmap_1.1.1           
##  [58] fansi_1.0.5              digest_0.6.33            timechange_0.2.0        
##  [61] R6_2.5.1                 colorspace_2.1-0         biomaRt_2.58.0          
##  [64] RSQLite_2.3.3            utf8_1.2.4               generics_0.1.3          
##  [67] prettyunits_1.2.0        httr_1.4.7               S4Arrays_1.2.0          
##  [70] pkgconfig_2.0.3          gtable_0.3.4             blob_1.2.4              
##  [73] impute_1.76.0            carData_3.0-5            RBGL_1.78.0             
##  [76] GSEABase_1.64.0          scales_1.3.0             png_0.1-8               
##  [79] rstudioapi_0.15.0        tzdb_0.4.0               rjson_0.2.21            
##  [82] curl_5.1.0               nlme_3.1-163             checkmate_2.3.0         
##  [85] cachem_1.0.8             foreign_0.8-85           restfulr_0.0.15         
##  [88] pillar_1.9.0             grid_4.3.2               vctrs_0.6.4             
##  [91] car_3.1-2                dbplyr_2.4.0             xtable_1.8-4            
##  [94] cluster_2.1.4            htmlTable_2.4.2          Rgraphviz_2.46.0        
##  [97] evaluate_0.23            GenomicFeatures_1.54.1   locfit_1.5-9.8          
## [100] cli_3.6.1                compiler_4.3.2           Rsamtools_2.18.0        
## [103] rlang_1.1.3              crayon_1.5.2             ggsignif_0.6.4          
## [106] plyr_1.8.9               stringi_1.8.2            viridisLite_0.4.2       
## [109] BiocParallel_1.36.0      munsell_0.5.0            lazyeval_0.2.2          
## [112] hms_1.1.3                bit64_4.0.5              statmod_1.5.0           
## [115] KEGGREST_1.42.0          highr_0.10               broom_1.0.5             
## [118] memoise_2.0.1            bslib_0.5.1              bit_4.0.5