Next week / Next steps
- Download one candidate series and its supplementary counts
- Document everything (session info, package versions)
## R version 4.5.2 (2025-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
## [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggrepel_0.9.6 edgeR_4.6.3 limma_3.64.3 reshape2_1.4.5
## [5] biomaRt_2.64.0 GEOquery_2.76.0 Biobase_2.68.0 BiocGenerics_0.54.1
## [9] generics_0.1.4 knitr_1.51 rmarkdown_2.30 readr_2.1.6
## [13] dplyr_1.1.4 ggplot2_4.0.1 DBI_1.2.3 GEOmetadb_1.70.0
## [17] RSQLite_2.4.5 R.utils_2.13.0 R.oo_1.27.1 R.methodsS3_1.8.2
##
## loaded via a namespace (and not attached):
## [1] httr2_1.2.2 rlang_1.1.6 magrittr_2.0.4
## [4] clue_0.3-66 GetoptLong_1.1.0 otel_0.2.0
## [7] matrixStats_1.5.0 compiler_4.5.2 png_0.1-8
## [10] vctrs_0.6.5 stringr_1.6.0 pkgconfig_2.0.3
## [13] shape_1.4.6.1 crayon_1.5.3 fastmap_1.2.0
## [16] dbplyr_2.5.1 XVector_0.48.0 labeling_0.4.3
## [19] tzdb_0.5.0 preprocessCore_1.70.0 UCSC.utils_1.4.0
## [22] purrr_1.2.0 bit_4.6.0 xfun_0.55
## [25] cachem_1.1.0 GenomeInfoDb_1.44.3 jsonlite_2.0.0
## [28] progress_1.2.3 blob_1.2.4 DelayedArray_0.34.1
## [31] prettyunits_1.2.0 parallel_4.5.2 cluster_2.1.8.1
## [34] R6_2.6.1 bslib_0.9.0 stringi_1.8.7
## [37] RColorBrewer_1.1-3 pkgload_1.4.1 jquerylib_0.1.4
## [40] GenomicRanges_1.60.0 bookdown_0.46 Rcpp_1.1.0
## [43] SummarizedExperiment_1.38.1 iterators_1.0.14 IRanges_2.42.0
## [46] rentrez_1.2.4 Matrix_1.7-4 tidyselect_1.2.1
## [49] yaml_2.3.11 rstudioapi_0.17.1 abind_1.4-8
## [52] doParallel_1.0.17 codetools_0.2-20 curl_7.0.0
## [55] plyr_1.8.9 lattice_0.22-7 tibble_3.3.0
## [58] withr_3.0.2 KEGGREST_1.48.1 S7_0.2.1
## [61] evaluate_1.0.5 BiocFileCache_2.16.2 xml2_1.5.1
## [64] circlize_0.4.17 Biostrings_2.76.0 pillar_1.11.1
## [67] BiocManager_1.30.27 filelock_1.0.3 rsconnect_1.7.0
## [70] MatrixGenerics_1.20.0 foreach_1.5.2 stats4_4.5.2
## [73] S4Vectors_0.46.0 hms_1.1.4 scales_1.4.0
## [76] glue_1.8.0 tools_4.5.2 data.table_1.18.0
## [79] locfit_1.5-9.12 XML_3.99-0.20 grid_4.5.2
## [82] tidyr_1.3.2 AnnotationDbi_1.70.0 colorspace_2.1-2
## [85] patchwork_1.3.2 GenomeInfoDbData_1.2.14 cli_3.6.5
## [88] rappdirs_0.3.3 S4Arrays_1.8.1 ComplexHeatmap_2.24.1
## [91] gtable_0.3.6 sass_0.4.10 digest_0.6.39
## [94] SparseArray_1.8.1 rjson_0.2.23 farver_2.1.2
## [97] memoise_2.0.1 htmltools_0.5.9 lifecycle_1.0.4
## [100] httr_1.4.7 GlobalOptions_0.1.3 statmod_1.5.1
## [103] bit64_4.6.0-1