1 Distance of samples by various metrics

1.1 Jaccard distance based on shared target genes

Figure 1 : Jaccard distance based on shared target genes. Here we plot the distance matrix between samples based on the Jaccard index computed for each pairwise sample based on how many genes the compared pair of samples co-overlap.

1.2 Clustering of samples based on overlaps with transcript features

Figure 2 : Clustering of samples based on overlaps with transcript features

2 Motif Discovery

Figure 3 : Feature specific motifs discovered for each sample

3 Feature Boundary Coverage Profiles

3.1 Smoothed line plots

Figure 4 : Feature boundary coverage profiles for each sample

3.2 PCA plots

3.2.1 transcripts

3.2.2 exons

3.2.3 promoters

3.2.4 fiveUTRs

3.2.5 introns

3.2.6 cds

3.2.7 threeUTRs

4 Acknowledgements

RCAS is developed in the group of Altuna Akalin (head of the Scientific Bioinformatics Platform) by Bora Uyar (Bioinformatics Scientist), Dilmurat Yusuf (Bioinformatics Scientist) and Ricardo Wurmus (System Administrator) at the Berlin Institute of Medical Systems Biology (BIMSB) at the Max-Delbrueck-Center for Molecular Medicine (MDC) in Berlin.

RCAS is developed as a bioinformatics service as part of the RNA Bioinformatics Center, which is one of the eight centers of the German Network for Bioinformatics Infrastructure (de.NBI).

5 Session Information

## R Under development (unstable) (2018-01-01 r74017)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS High Sierra 10.13.3
## 
## Matrix products: default
## BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
##  [1] grid      stats4    parallel  stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] RCAS_1.5.2                        motifRG_1.23.0                   
##  [3] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.47.1                  
##  [5] rtracklayer_1.39.4                GenomicRanges_1.31.3             
##  [7] GenomeInfoDb_1.15.1               seqLogo_1.45.0                   
##  [9] Biostrings_2.47.1                 XVector_0.19.1                   
## [11] topGO_2.31.0                      SparseM_1.77                     
## [13] GO.db_3.5.0                       AnnotationDbi_1.41.4             
## [15] IRanges_2.13.5                    S4Vectors_0.17.17                
## [17] Biobase_2.39.1                    graph_1.57.1                     
## [19] BiocGenerics_0.25.1               data.table_1.10.4-3              
## [21] DT_0.2                            plotly_4.7.1                     
## [23] ggplot2_2.2.1                    
## 
## loaded via a namespace (and not attached):
##  [1] nlme_3.1-135               bitops_1.0-6              
##  [3] matrixStats_0.52.2         bit64_0.9-7               
##  [5] RColorBrewer_1.1-2         progress_1.1.2            
##  [7] httr_1.3.1                 rprojroot_1.3-2           
##  [9] tools_3.5.0                backports_1.1.2           
## [11] R6_2.2.2                   KernSmooth_2.23-15        
## [13] mgcv_1.8-22                DBI_0.7                   
## [15] lazyeval_0.2.1             colorspace_1.3-2          
## [17] seqPattern_1.11.0          tidyselect_0.2.3          
## [19] prettyunits_1.0.2          RMySQL_0.10.13            
## [21] bit_1.1-12                 compiler_3.5.0            
## [23] genomation_1.11.0          DelayedArray_0.5.15       
## [25] labeling_0.3               scales_0.5.0              
## [27] readr_1.1.1                proxy_0.4-21              
## [29] pbapply_1.3-3              stringr_1.2.0             
## [31] digest_0.6.13              Rsamtools_1.31.1          
## [33] rmarkdown_1.8              pkgconfig_2.0.1           
## [35] htmltools_0.3.6            plotrix_3.7               
## [37] htmlwidgets_0.9            rlang_0.1.6               
## [39] RSQLite_2.0                impute_1.53.0             
## [41] shiny_1.0.5                bindr_0.1                 
## [43] jsonlite_1.5               crosstalk_1.0.0           
## [45] BiocParallel_1.13.1        dplyr_0.7.4               
## [47] RCurl_1.95-4.10            magrittr_1.5              
## [49] GenomeInfoDbData_1.1.0     Matrix_1.2-12             
## [51] Rcpp_0.12.14               munsell_0.4.3             
## [53] yaml_2.1.16                stringi_1.1.6             
## [55] SummarizedExperiment_1.9.5 zlibbioc_1.25.0           
## [57] org.Hs.eg.db_3.5.0         plyr_1.8.4                
## [59] ggseqlogo_0.1              blob_1.1.0                
## [61] lattice_0.20-35            cowplot_0.9.2             
## [63] GenomicFeatures_1.31.1     hms_0.4.0                 
## [65] knitr_1.18                 pillar_1.0.1              
## [67] reshape2_1.4.3             biomaRt_2.35.5            
## [69] XML_3.98-1.9               glue_1.2.0                
## [71] evaluate_0.10.1            httpuv_1.3.5              
## [73] gtable_0.2.0               purrr_0.2.4               
## [75] tidyr_0.7.2                assertthat_0.2.0          
## [77] gridBase_0.4-7             mime_0.5                  
## [79] xtable_1.8-2               viridisLite_0.2.0         
## [81] pheatmap_1.0.8             tibble_1.4.1              
## [83] GenomicAlignments_1.15.2   memoise_1.1.0             
## [85] bindrcpp_0.2