DimensionReduction_Clustering
Yasin Kaymaz
1/30/2019
Last updated: 2019-04-18
Checks: 6 0
Knit directory: Harvard-RosenbrockLab/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 2bd3ebb | Yasin Kaymaz | 2019-04-18 | flip-flops commit |
| html | 4277c88 | Yasin Kaymaz | 2019-03-15 | Build site. |
| 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;
In the analysis, I excluded E15.5 cells as requested by CNSDR and done the rest of analysis with only P7 mice cells.
PCA plots
UMAP plots
Cells are colored by mouse brain region, and cell subsets, respectively.
| 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 10.14.4
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] forcats_0.4.0 stringr_1.4.0 purrr_0.3.2 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_1.1.4
[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] mvtnorm_1.0-10 bibtex_0.4.2 Rcpp_1.0.1
[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
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[64] nnet_7.3-12 labeling_0.3 tidyselect_0.2.5
[67] rlang_0.3.4 reshape2_1.4.3 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
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[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
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[97] lattice_0.20-35 trimcluster_0.1-2.1 pillar_1.3.1
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[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