Last updated: 2019-03-15

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Rmd ae57569 Yasin Kaymaz 2019-03-15 isoform results
html 1abd5c7 Yasin Kaymaz 2019-03-15 Build site.
Rmd dbac3ec Yasin Kaymaz 2019-03-15 isoform results

Gene expression distributions among cells in each group

After count processing and filtration, I group all cells based on mouse age, brain region, and cell subsets. Violin plots show normalized expression distribution of the given gene in each cell (black dots) binned in various groups. y-axis is in log2 scale!

Genes of interest are “Gria1”,“Gria4”,“Grm4”, and “Gpr83”.

Cells are grouped based on mouse age

Version Author Date
1abd5c7 Yasin Kaymaz 2019-03-15

Cells are grouped based on brain region

Cells are grouped based on cell subset

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sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin17.5.0 (64-bit)
Running under: macOS  10.14.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Seurat_2.3.4    Matrix_1.2-14   cowplot_0.9.4   here_0.1       
 [5] forcats_0.4.0   stringr_1.4.0   dplyr_0.8.0.1   purrr_0.3.1    
 [9] readr_1.3.1     tidyr_0.8.3     tibble_2.0.1    tidyverse_1.2.1
[13] DT_0.5          plotly_4.8.0    ggplot2_3.1.0  

loaded via a namespace (and not attached):
  [1] readxl_1.3.1        snow_0.4-3          backports_1.1.2    
  [4] Hmisc_4.2-0         workflowr_1.2.0     plyr_1.8.4         
  [7] igraph_1.2.4        lazyeval_0.2.1      splines_3.5.0      
 [10] digest_0.6.18       foreach_1.4.4       htmltools_0.3.6    
 [13] lars_1.2            gdata_2.18.0        magrittr_1.5       
 [16] checkmate_1.9.1     cluster_2.0.7-1     mixtools_1.1.0     
 [19] ROCR_1.0-7          modelr_0.1.4        R.utils_2.8.0      
 [22] colorspace_1.4-0    rvest_0.3.2         haven_2.1.0        
 [25] crayon_1.3.4        jsonlite_1.6        survival_2.42-6    
 [28] zoo_1.8-4           iterators_1.0.10    ape_5.2            
 [31] glue_1.3.1          gtable_0.2.0        kernlab_0.9-27     
 [34] prabclus_2.2-7      DEoptimR_1.0-8      scales_1.0.0       
 [37] mvtnorm_1.0-10      bibtex_0.4.2        Rcpp_1.0.0         
 [40] metap_1.1           dtw_1.20-1          viridisLite_0.3.0  
 [43] htmlTable_1.13.1    reticulate_1.11.1   foreign_0.8-70     
 [46] bit_1.1-14          proxy_0.4-23        mclust_5.4.3       
 [49] SDMTools_1.1-221    Formula_1.2-3       tsne_0.1-3         
 [52] stats4_3.5.0        htmlwidgets_1.3     httr_1.4.0         
 [55] gplots_3.0.1.1      RColorBrewer_1.1-2  fpc_2.1-11.1       
 [58] acepack_1.4.1       modeltools_0.2-22   ica_1.0-2          
 [61] pkgconfig_2.0.2     R.methodsS3_1.7.1   flexmix_2.3-15     
 [64] nnet_7.3-12         labeling_0.3        reshape2_1.4.3     
 [67] tidyselect_0.2.5    rlang_0.3.1         munsell_0.5.0      
 [70] cellranger_1.1.0    tools_3.5.0         cli_1.0.1          
 [73] generics_0.0.2      broom_0.5.1         ggridges_0.5.1     
 [76] evaluate_0.10.1     yaml_2.2.0          npsurv_0.4-0       
 [79] knitr_1.20          bit64_0.9-7         fs_1.2.6           
 [82] fitdistrplus_1.0-14 robustbase_0.93-3   caTools_1.17.1.2   
 [85] RANN_2.6.1          pbapply_1.4-0       nlme_3.1-137       
 [88] whisker_0.3-2       R.oo_1.22.0         xml2_1.2.0         
 [91] hdf5r_1.0.1         compiler_3.5.0      rstudioapi_0.9.0   
 [94] png_0.1-7           lsei_1.2-0          stringi_1.2.4      
 [97] lattice_0.20-35     trimcluster_0.1-2.1 pillar_1.3.1       
[100] Rdpack_0.10-1       lmtest_0.9-36       data.table_1.12.0  
[103] bitops_1.0-6        irlba_2.3.3         gbRd_0.4-11        
[106] R6_2.4.0            latticeExtra_0.6-28 KernSmooth_2.23-15 
[109] gridExtra_2.3       codetools_0.2-15    MASS_7.3-50        
[112] gtools_3.8.1        assertthat_0.2.0    rprojroot_1.3-2    
[115] withr_2.1.2         diptest_0.75-7      parallel_3.5.0     
[118] doSNOW_1.0.16       hms_0.4.2           grid_3.5.0         
[121] rpart_4.1-13        class_7.3-14        rmarkdown_1.10     
[124] segmented_0.5-3.0   Rtsne_0.15          git2r_0.24.0       
[127] lubridate_1.7.4     base64enc_0.1-3