Retrieve the fastq files from SRA and then align to the canine genome. Instructions to download the fastq files can be found in 📁 input. The alignment code is currently not provided (used a default Cell Ranger workflow), but can be shared if desired.
Clone this repository (git clone https://github.com/dyammons/canine_duodenal_atlas.git) then follow the instructions in 📁 input to obtain count matrices from NCBI GEO to get the count matricies into the input directory. Start with 1_preProcessData.R then move through the scripts in increasing figure number.
Clone this repository (git clone https://github.com/dyammons/canine_duodenal_atlas.git) then follow the instructions in 📁 input to obtain processed Seurat objects from Zenodo to get the .rds files in the /output/s3/ directory. These objects can be loaded in for scripts 3-9.
This work was completed on the UC boulder Alpine supercomputer on a Linux operating system. All code was run in a conda environment and I am happy to share the .yml file upon request.
Otherwise, see below for packages loaded into the system.
> 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] circlize_0.4.16 singleseqgset_0.1.2.9000
[3] Matrix_1.5-1 copykat_1.0.5
[5] infercnv_1.10.1 ComplexHeatmap_2.13.2
[7] ggtree_3.2.1 ape_5.7-1
[9] scuttle_1.4.0 scRNAseq_2.8.0
[11] ggpubr_0.4.0 slingshot_2.7.0
[13] TrajectoryUtils_1.2.0 SingleCellExperiment_1.16.0
[15] princurve_2.1.6 clusterProfiler_4.2.2
[17] msigdbr_7.5.1 ggsankey_0.0.99999
[19] lemon_0.4.5 reshape_0.8.9
[21] viridis_0.6.2 viridisLite_0.4.1
[23] SingleR_1.8.1 SeuratDisk_0.0.0.9019
[25] RColorBrewer_1.1-3 pheatmap_1.0.12
[27] DESeq2_1.34.0 SummarizedExperiment_1.24.0
[29] Biobase_2.54.0 MatrixGenerics_1.6.0
[31] matrixStats_1.0.0 GenomicRanges_1.46.1
[33] GenomeInfoDb_1.30.1 IRanges_2.28.0
[35] S4Vectors_0.32.4 BiocGenerics_0.40.0
[37] colorspace_2.0-3 ggrepel_0.9.1
[39] cowplot_1.1.1 scales_1.2.1
[41] patchwork_1.1.2 DoubletFinder_2.0.3
[43] clustree_0.4.4 ggraph_2.0.5
[45] forcats_0.5.2 stringr_1.4.1
[47] dplyr_1.0.10 purrr_0.3.5
[49] readr_2.1.2 tidyr_1.2.1
[51] tibble_3.1.8 ggplot2_3.3.6
[53] tidyverse_1.3.1 SeuratObject_4.1.3
[55] 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] argparse_2.2.2 GOSemSim_2.20.0
[13] rlang_1.0.6 XVector_0.34.0
[15] ROCR_1.0-11 readxl_1.4.1
[17] irlba_2.3.5 limma_3.50.3
[19] filelock_1.0.2 BiocParallel_1.28.3
[21] rjson_0.2.21 bit64_4.0.5
[23] glue_1.6.2 sctransform_0.3.5
[25] parallel_4.1.1 spatstat.sparse_3.0-0
[27] AnnotationDbi_1.56.2 DOSE_3.20.1
[29] spatstat.geom_3.0-5 haven_2.4.3
[31] tidyselect_1.2.0 fitdistrplus_1.1-8
[33] XML_3.99-0.12 zoo_1.8-9
[35] GenomicAlignments_1.30.0 xtable_1.8-4
[37] magrittr_2.0.3 phyclust_0.1-32
[39] cli_3.6.0 zlibbioc_1.40.0
[41] rstudioapi_0.14 miniUI_0.1.1.1
[43] sp_1.5-1 rjags_4-13
[45] fastmatch_1.1-3 lambda.r_1.2.4
[47] ensembldb_2.18.3 treeio_1.18.1
[49] shiny_1.7.1 BiocSingular_1.10.0
[51] xfun_0.39 clue_0.3-62
[53] cluster_2.1.4 caTools_1.18.2
[55] tidygraph_1.2.2 KEGGREST_1.34.0
[57] interactiveDisplayBase_1.32.0 listenv_0.8.0
[59] Biostrings_2.62.0 png_0.1-7
[61] future_1.29.0 withr_2.5.0
[63] bitops_1.0-7 ggforce_0.4.1
[65] plyr_1.8.7 cellranger_1.1.0
[67] AnnotationFilter_1.18.0 coda_0.19-4
[69] pillar_1.8.1 gplots_3.1.3
[71] GlobalOptions_0.1.2 cachem_1.0.6
[73] GenomicFeatures_1.46.5 multcomp_1.4-20
[75] fs_1.5.2 hdf5r_1.3.8
[77] GetoptLong_1.0.5 DelayedMatrixStats_1.16.0
[79] vctrs_0.5.1 ellipsis_0.3.2
[81] generics_0.1.3 tools_4.1.1
[83] munsell_0.5.0 tweenr_2.0.2
[85] fgsea_1.20.0 DelayedArray_0.20.0
[87] fastmap_1.1.0 compiler_4.1.1
[89] abind_1.4-5 httpuv_1.6.5
[91] rtracklayer_1.54.0 ExperimentHub_2.2.1
[93] plotly_4.10.1 GenomeInfoDbData_1.2.7
[95] gridExtra_2.3 edgeR_3.36.0
[97] lattice_0.20-45 deldir_1.0-6
[99] utf8_1.2.2 later_1.3.0
[101] BiocFileCache_2.2.1 jsonlite_1.8.3
[103] ScaledMatrix_1.2.0 tidytree_0.3.9
[105] pbapply_1.5-0 carData_3.0-5
[107] sparseMatrixStats_1.6.0 genefilter_1.76.0
[109] lazyeval_0.2.2 promises_1.2.0.1
[111] car_3.1-0 doParallel_1.0.17
[113] goftest_1.2-3 spatstat.utils_3.0-1
[115] reticulate_1.34.0 sandwich_3.0-2
[117] Rtsne_0.16 downloader_0.4
[119] uwot_0.1.14 igraph_1.5.1
[121] survival_3.4-0 yaml_2.3.6
[123] htmltools_0.5.3 memoise_2.0.1
[125] modeltools_0.2-23 BiocIO_1.4.0
[127] locfit_1.5-9.6 graphlayouts_0.8.3
[129] digest_0.6.30 assertthat_0.2.1
[131] mime_0.12 rappdirs_0.3.3
[133] futile.options_1.0.1 RSQLite_2.2.18
[135] yulab.utils_0.0.5 future.apply_1.10.0
[137] data.table_1.14.4 blob_1.2.3
[139] futile.logger_1.4.3 splines_4.1.1
[141] AnnotationHub_3.2.2 ProtGenerics_1.26.0
[143] RCurl_1.98-1.12 broom_1.0.1
[145] hms_1.1.2 modelr_0.1.8
[147] BiocManager_1.30.19 shape_1.4.6
[149] libcoin_1.0-9 aplot_0.1.2
[151] coin_1.4-2 Rcpp_1.0.11
[153] RANN_2.6.1 mvtnorm_1.1-3
[155] enrichplot_1.14.2 fansi_1.0.3
[157] tzdb_0.3.0 parallelly_1.32.1
[159] R6_2.5.1 ggridges_0.5.4
[161] lifecycle_1.0.3 formatR_1.12
[163] curl_4.3.3 ggsignif_0.6.4
[165] leiden_0.4.3 fastcluster_1.2.3
[167] DO.db_2.9 qvalue_2.26.0
[169] TH.data_1.1-1 RcppAnnoy_0.0.20
[171] iterators_1.0.14 spatstat.explore_3.0-5
[173] htmlwidgets_1.5.4 beachmat_2.10.0
[175] polyclip_1.10-4 biomaRt_2.50.3
[177] shadowtext_0.1.1 timechange_0.1.1
[179] gridGraphics_0.5-1 rvest_1.0.3
[181] globals_0.16.1 spatstat.random_3.1-3
[183] progressr_0.11.0 codetools_0.2-18
[185] lubridate_1.9.0 GO.db_3.14.0
[187] gtools_3.9.3 prettyunits_1.1.1
[189] dbplyr_2.1.1 gtable_0.3.1
[191] DBI_1.1.3 ggfun_0.0.8
[193] tensor_1.5 httr_1.4.4
[195] KernSmooth_2.23-20 stringi_1.7.8
[197] progress_1.2.2 reshape2_1.4.4
[199] farver_2.1.1 annotate_1.72.0
[201] xml2_1.3.3 BiocNeighbors_1.12.0
[203] restfulr_0.0.15 geneplotter_1.72.0
[205] ggplotify_0.1.0 scattermore_0.8
[207] BiocVersion_3.14.0 bit_4.0.4
[209] scatterpie_0.1.7 spatstat.data_3.0-0
[211] pkgconfig_2.0.3 babelgene_22.9
[213] rstatix_0.7.0 knitr_1.40