Last updated: 2019-04-23

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Knit directory: Harvard-RosenbrockLab/

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File Version Author Date Message
Rmd 0ca3f62 Yasin Kaymaz 2019-04-23 annotated with cell types
html 1df9791 Yasin Kaymaz 2019-04-19 Build site.
Rmd d4af5c3 Yasin Kaymaz 2019-04-19 small edits
html bf98d10 Yasin Kaymaz 2019-04-18 Build site.
Rmd c9a6dac Yasin Kaymaz 2019-04-18 flip-flops commit
html 7203af5 Yasin Kaymaz 2019-04-18 Build site.
Rmd 2bd3ebb Yasin Kaymaz 2019-04-18 flip-flops commit

Cumulative gene expression:

Version Author Date
7203af5 Yasin Kaymaz 2019-04-18

This figure shows the distribution of normalized expression (log2) of each glutamate ionotropic receptor AMPA genes in each cell group identified by Hook et al. The horizontal lines in bars = Median, Red dots = outlier cells,

Isoforms

Gria1 Isoforms:

‘hGluA1i Flip’ = ENSMUST00000036315.15_Gria1-201 ‘hGluA1o Flop’ = ENSMUST00000094179.10_Gria1-202

Version Author Date
7203af5 Yasin Kaymaz 2019-04-18

The heatmap shows the percent usage of each isoform in cells. Columns are cells and rows are all possible isoforms. Color scale from dark-blue to dark-red represent 0% to 100%. The green color annotation on top of the heatmap is the cumulative expression value for the given gene in that cell.

Version Author Date
7203af5 Yasin Kaymaz 2019-04-18

Gria2 Isoforms:

‘hGluA2o Flop’ = ENSMUST00000075316.9_Gria2-201 ‘hGluA2i Q/R Mut Flip’ = ENSMUST00000107745.7_Gria2-202

Version Author Date
7203af5 Yasin Kaymaz 2019-04-18

Version Author Date
7203af5 Yasin Kaymaz 2019-04-18

Gria3 Isoforms:

‘hGluA3o Flop’ = ENSMUST00000165288.1_Gria3-209 ‘hGluA3i Flip’ = ENSMUST00000076349.11_Gria3-201

Version Author Date
7203af5 Yasin Kaymaz 2019-04-18

Version Author Date
7203af5 Yasin Kaymaz 2019-04-18

Gria4 Isoforms:

‘hGluA4o Flop’ = ENSMUST00000027020.12_Gria4-201 ‘hGluA4i Flip’ = ENSMUST00000063508.14_Gria4-202

Version Author Date
7203af5 Yasin Kaymaz 2019-04-18

Version Author Date
7203af5 Yasin Kaymaz 2019-04-18 


sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin17.5.0 (64-bit)
Running under: macOS  10.14.4

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_0.3.2    
 [9] readr_1.3.1     tidyr_0.8.3     tibble_2.0.1    tidyverse_1.2.1
[13] reshape2_1.4.3  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_1.1.4    
  [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] pheatmap_1.0.12     mvtnorm_1.0-10      bibtex_0.4.2       
 [40] Rcpp_1.0.1          metap_1.1           dtw_1.20-1         
 [43] viridisLite_0.3.0   htmlTable_1.13.1    reticulate_1.11.1  
 [46] foreign_0.8-70      bit_1.1-14          proxy_0.4-23       
 [49] mclust_5.4.3        SDMTools_1.1-221    Formula_1.2-3      
 [52] tsne_0.1-3          stats4_3.5.0        htmlwidgets_1.3    
 [55] httr_1.4.0          gplots_3.0.1.1      RColorBrewer_1.1-2 
 [58] fpc_2.1-11.1        acepack_1.4.1       modeltools_0.2-22  
 [61] ica_1.0-2           pkgconfig_2.0.2     R.methodsS3_1.7.1  
 [64] flexmix_2.3-15      nnet_7.3-12         labeling_0.3       
 [67] tidyselect_0.2.5    rlang_0.3.4         munsell_0.5.0      
 [70] cellranger_1.1.0    tools_3.5.0         cli_1.1.0          
 [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_1.2.7           
 [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_0.10    
 [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_0.2.1    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_0.25.2       
[127] lubridate_1.7.4     base64enc_0.1-3