DimensionReduction_Clustering
Yasin Kaymaz
1/30/2019
Last updated: 2019-03-15
Checks: 6 0
Knit directory: Harvard-RosenbrockLab/
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| File | Version | Author | Date | Message |
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| Rmd | b85db50 | Yasin Kaymaz | 2019-03-15 | isoform results |
| html | de005bf | Yasin Kaymaz | 2019-03-15 | Build site. |
| html | abeab71 | Yasin Kaymaz | 2019-03-15 | Build site. |
| 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 |
| html | 49c0cce | Yasin Kaymaz | 2019-03-06 | Build site. |
| html | 3d2c5f6 | Yasin Kaymaz | 2019-03-06 | Build site. |
| html | f4d0605 | Yasin Kaymaz | 2019-03-05 | Build site. |
| Rmd | 6ead7d0 | Yasin Kaymaz | 2019-03-05 | violin plots |
| html | ced17ea | Yasin Kaymaz | 2019-03-05 | Build site. |
| Rmd | 066a7e8 | Yasin Kaymaz | 2019-03-05 | violin plots |
| html | c534f45 | Yasin Kaymaz | 2019-03-04 | Build site. |
| html | a1bf7ee | Yasin Kaymaz | 2019-03-04 | Build site. |
| Rmd | 1be7385 | Yasin Kaymaz | 2019-03-04 | initial commit |
Clustering analysis of all cells in the Hook 2018 study
In each of these plots, colored dots represent individual cells. Analysis was done using only highly variable genes. Cell annotation are projected from original publication.
Three brain regions cells are taken from:
midbrain, MB; forebrain, FB; olfactory bulb, OB;
PCA plots
Cells are colored by mouse age, brain region, and cell subsets, respectively.
| Version | Author | Date |
|---|---|---|
| 1abd5c7 | Yasin Kaymaz | 2019-03-15 |
tSNE plots
Cells are colored by mouse age, brain region, and cell subsets, respectively.
| Version | Author | Date |
|---|---|---|
| abeab71 | Yasin Kaymaz | 2019-03-15 |
| Version | Author | Date |
|---|---|---|
| abeab71 | Yasin Kaymaz | 2019-03-15 |
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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] forcats_0.4.0 stringr_1.4.0 purrr_0.3.1 readr_1.3.1
[5] tidyr_0.8.3 tibble_2.0.1 tidyverse_1.2.1 dplyr_0.8.0.1
[9] Seurat_2.3.4 Matrix_1.2-14 cowplot_0.9.4 here_0.1
[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 stats4_3.5.0
[52] tsne_0.1-3 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 tidyselect_0.2.5
[67] rlang_0.3.1 reshape2_1.4.3 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