This GitHub repository contains all the analysis code used in, "Characterization of canine tumor-infiltrating leukocyte transcriptomic signatures reveals conserved expression patterns with human osteosarcoma."
If you use our raw/processed data, extract data using the UCSC Cell Browser portal, or use portions of our code in your analysis, please cite:
accepted, publication pending
If you have any questions or concerns, please submit an issue, contact the corresponding author(s), and/or contact Dylan Ammons at dylan.ammons @ colostate dot edu.
- 📁 scripts contains the analysis code, source file, and metadata used to complete analysis
The proccessed dataset is avaliable for browsing via the UCSC Cell Browser portal. Using the portal you can explore feature expression throughout the dataset as well as obtain the transcriptomic signatures of each cell type though an interactive webpage.
Link to the dataset: https://canine-tils-blood.cells.ucsc.edu
Link to UCSC Cell Browser documentation: https://cellbrowser.readthedocs.io/en/master/
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.4 (Ootpa)
Matrix products: default
BLAS/LAPACK: /projects/dyammons@colostate.edu/software/anaconda/envs/r_env/lib/libopenblasp-r0.3.18.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C
[4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ComplexHeatmap_2.13.2 ggtree_3.2.1
[3] ape_5.7-1 scuttle_1.4.0
[5] scRNAseq_2.8.0 ggpubr_0.4.0
[7] slingshot_2.7.0 TrajectoryUtils_1.2.0
[9] SingleCellExperiment_1.16.0 princurve_2.1.6
[11] clusterProfiler_4.2.2 msigdbr_7.5.1
[13] ggsankey_0.0.99999 lemon_0.4.5
[15] reshape_0.8.9 viridis_0.6.2
[17] viridisLite_0.4.1 SingleR_1.8.1
[19] SeuratDisk_0.0.0.9019 RColorBrewer_1.1-3
[21] pheatmap_1.0.12 DESeq2_1.34.0
[23] SummarizedExperiment_1.24.0 Biobase_2.54.0
[25] MatrixGenerics_1.6.0 matrixStats_1.0.0
[27] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1
[29] IRanges_2.28.0 S4Vectors_0.32.4
[31] BiocGenerics_0.40.0 colorspace_2.0-3
[33] ggrepel_0.9.1 cowplot_1.1.1
[35] scales_1.3.0 patchwork_1.3.0.9000
[37] DoubletFinder_2.0.3 clustree_0.4.4
[39] ggraph_2.0.5 forcats_0.5.2
[41] stringr_1.4.1 dplyr_1.0.10
[43] purrr_0.3.5 readr_2.1.2
[45] tidyr_1.2.1 tibble_3.1.8
[47] ggplot2_3.3.6 tidyverse_1.3.1
[49] SeuratObject_4.1.3 Seurat_4.3.0
loaded via a namespace (and not attached):
[1] rsvd_1.0.5 ica_1.0-3
[3] Rsamtools_2.10.0 foreach_1.5.2
[5] lmtest_0.9-40 crayon_1.5.2
[7] MASS_7.3-58.1 nlme_3.1-160
[9] backports_1.4.1 reprex_2.0.1
[11] GOSemSim_2.20.0 rlang_1.0.6
[13] XVector_0.34.0 ROCR_1.0-11
[15] readxl_1.4.1 irlba_2.3.5
[17] filelock_1.0.2 BiocParallel_1.37.1
[19] rjson_0.2.21 bit64_4.0.5
[21] glue_1.6.2 sctransform_0.3.5
[23] parallel_4.1.1 spatstat.sparse_3.0-0
[25] AnnotationDbi_1.56.2 DOSE_3.20.1
[27] spatstat.geom_3.0-5 haven_2.4.3
[29] tidyselect_1.2.0 fitdistrplus_1.1-8
[31] XML_3.99-0.12 zoo_1.8-9
[33] GenomicAlignments_1.30.0 xtable_1.8-4
[35] magrittr_2.0.3 cli_3.6.0
[37] zlibbioc_1.40.0 rstudioapi_0.14
[39] miniUI_0.1.1.1 sp_1.5-1
[41] fastmatch_1.1-3 ensembldb_2.18.3
[43] treeio_1.18.1 shiny_1.7.1
[45] BiocSingular_1.10.0 xfun_0.39
[47] clue_0.3-62 cluster_2.1.4
[49] tidygraph_1.2.2 KEGGREST_1.34.0
[51] interactiveDisplayBase_1.32.0 listenv_0.8.0
[53] Biostrings_2.62.0 png_0.1-7
[55] future_1.29.0 withr_2.5.0
[57] bitops_1.0-7 ggforce_0.4.1
[59] plyr_1.8.7 cellranger_1.1.0
[61] AnnotationFilter_1.18.0 pillar_1.8.1
[63] GlobalOptions_0.1.2 cachem_1.0.6
[65] GenomicFeatures_1.46.5 fs_1.5.2
[67] hdf5r_1.3.8 GetoptLong_1.0.5
[69] DelayedMatrixStats_1.16.0 vctrs_0.5.1
[71] ellipsis_0.3.2 generics_0.1.3
[73] tools_4.1.1 munsell_0.5.0
[75] tweenr_2.0.2 fgsea_1.20.0
[77] DelayedArray_0.20.0 fastmap_1.1.0
[79] compiler_4.1.1 abind_1.4-5
[81] httpuv_1.6.5 rtracklayer_1.54.0
[83] ExperimentHub_2.2.1 plotly_4.10.1
[85] GenomeInfoDbData_1.2.7 gridExtra_2.3
[87] lattice_0.20-45 deldir_1.0-6
[89] utf8_1.2.2 later_1.3.0
[91] BiocFileCache_2.2.1 jsonlite_1.8.3
[93] ScaledMatrix_1.2.0 tidytree_0.3.9
[95] pbapply_1.5-0 carData_3.0-5
[97] sparseMatrixStats_1.6.0 genefilter_1.76.0
[99] lazyeval_0.2.2 promises_1.2.0.1
[101] car_3.1-0 doParallel_1.0.17
[103] R.utils_2.12.1 goftest_1.2-3
[105] spatstat.utils_3.0-1 reticulate_1.34.0
[107] Rtsne_0.16 downloader_0.4
[109] uwot_0.1.14 igraph_1.5.1
[111] survival_3.4-0 yaml_2.3.6
[113] htmltools_0.5.3 memoise_2.0.1
[115] BiocIO_1.4.0 locfit_1.5-9.6
[117] graphlayouts_0.8.3 digest_0.6.30
[119] assertthat_0.2.1 mime_0.12
[121] rappdirs_0.3.3 RSQLite_2.2.18
[123] yulab.utils_0.0.5 future.apply_1.10.0
[125] data.table_1.14.4 blob_1.2.3
[127] R.oo_1.25.0 splines_4.1.1
[129] AnnotationHub_3.2.2 ProtGenerics_1.26.0
[131] RCurl_1.98-1.12 broom_1.0.1
[133] hms_1.1.2 modelr_0.1.8
[135] BiocManager_1.30.19 shape_1.4.6
[137] aplot_0.1.2 Rcpp_1.0.11
[139] RANN_2.6.1 circlize_0.4.16
[141] enrichplot_1.14.2 fansi_1.0.3
[143] tzdb_0.3.0 parallelly_1.32.1
[145] R6_2.5.1 ggridges_0.5.4
[147] lifecycle_1.0.3 curl_4.3.3
[149] ggsignif_0.6.4 leiden_0.4.3
[151] DO.db_2.9 Matrix_1.5-1
[153] qvalue_2.26.0 RcppAnnoy_0.0.20
[155] iterators_1.0.14 spatstat.explore_3.0-5
[157] htmlwidgets_1.5.4 beachmat_2.10.0
[159] polyclip_1.10-4 biomaRt_2.50.3
[161] shadowtext_0.1.1 timechange_0.1.1
[163] gridGraphics_0.5-1 rvest_1.0.3
[165] globals_0.16.1 spatstat.random_3.1-3
[167] progressr_0.11.0 codetools_0.2-18
[169] lubridate_1.9.0 GO.db_3.14.0
[171] prettyunits_1.1.1 dbplyr_2.1.1
[173] R.methodsS3_1.8.2 gtable_0.3.1
[175] DBI_1.1.3 ggfun_0.0.8
[177] tensor_1.5 httr_1.4.4
[179] KernSmooth_2.23-20 stringi_1.7.8
[181] progress_1.2.2 reshape2_1.4.4
[183] farver_2.1.1 annotate_1.72.0
[185] xml2_1.3.3 BiocNeighbors_1.12.0
[187] restfulr_0.0.15 geneplotter_1.72.0
[189] ggplotify_0.1.0 scattermore_0.8
[191] BiocVersion_3.14.0 bit_4.0.4
[193] scatterpie_0.1.7 spatstat.data_3.0-0
[195] pkgconfig_2.0.3 babelgene_22.9
[197] rstatix_0.7.0 knitr_1.40