The RNAseq Analysis Source Code
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.6 LTS
Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] survminer_0.4.6 ggpubr_0.2.4
[3] magrittr_1.5 survival_3.1-8
[5] BiocParallel_1.12.0 WGCNA_1.68
[7] fastcluster_1.1.25 dynamicTreeCut_1.63-1
[9] dendextend_1.13.2 VennDiagram_1.6.20
[11] futile.logger_1.4.3 pheatmap_1.0.12
[13] ReactomePA_1.22.0 DOSE_3.4.0
[15] stringr_1.4.0 ggplot2_3.3.2
[17] edgeR_3.20.9 limma_3.34.9
[19] DESeq2_1.18.1 SummarizedExperiment_1.8.1
[21] DelayedArray_0.4.1 matrixStats_0.56.0
[23] ensembldb_2.2.2 AnnotationFilter_1.2.0
[25] GenomicFeatures_1.30.3 AnnotationDbi_1.40.0
[27] Biobase_2.38.0 GenomicRanges_1.30.3
[29] GenomeInfoDb_1.14.0 IRanges_2.12.0
[31] S4Vectors_0.16.0 AnnotationHub_2.10.1
[33] BiocGenerics_0.24.0
loaded via a namespace (and not attached):
[1] backports_1.1.8 Hmisc_4.3-0
[3] fastmatch_1.1-0 plyr_1.8.5
[5] igraph_1.2.4.2 lazyeval_0.2.2
[7] splines_3.4.4 robust_0.4-18.1
[9] digest_0.6.25 foreach_1.4.7
[11] BiocInstaller_1.28.0 htmltools_0.4.0
[13] GOSemSim_2.4.1 viridis_0.5.1
[15] GO.db_3.5.0 checkmate_1.9.4
[17] memoise_1.1.0 fit.models_0.5-14
[19] doParallel_1.0.15 cluster_2.1.0
[21] Biostrings_2.46.0 annotate_1.56.2
[23] prettyunits_1.1.1 colorspace_1.4-1
[25] rrcov_1.4-7 blob_1.2.0
[27] rappdirs_0.3.1 xfun_0.11
[29] dplyr_1.0.0 crayon_1.3.4
[31] RCurl_1.98-1.2 graph_1.56.0
[33] genefilter_1.60.0 impute_1.52.0
[35] zoo_1.8-6 iterators_1.0.12
[37] glue_1.4.1 gtable_0.3.0
[39] zlibbioc_1.24.0 XVector_0.18.0
[41] graphite_1.24.1 DEoptimR_1.0-8
[43] scales_1.1.1 mvtnorm_1.0-7
[45] futile.options_1.0.1 DBI_1.1.0
[47] Rcpp_1.0.5 viridisLite_0.3.0
[49] xtable_1.8-4 progress_1.2.2
[51] htmlTable_1.13.3 foreign_0.8-72
[53] bit_1.1-14 reactome.db_1.62.0
[55] km.ci_0.5-2 preprocessCore_1.40.0
[57] Formula_1.2-3 htmlwidgets_1.5.1
[59] httr_1.4.1 fgsea_1.4.1
[61] RColorBrewer_1.1-2 acepack_1.4.1
[63] ellipsis_0.3.1 pkgconfig_2.0.3
[65] XML_3.98-1.20 nnet_7.3-12
[67] locfit_1.5-9.1 tidyselect_1.1.0
[69] rlang_0.4.7 reshape2_1.4.3
[71] later_1.0.0 munsell_0.5.0
[73] tools_3.4.4 generics_0.0.2
[75] RSQLite_2.1.5 broom_0.5.2
[77] fastmap_1.0.1 yaml_2.2.0
[79] knitr_1.26 bit64_0.9-7
[81] robustbase_0.93-5 survMisc_0.5.5
[83] purrr_0.3.4 nlme_3.1-142
[85] mime_0.8 formatR_1.7
[87] DO.db_2.9 biomaRt_2.34.2
[89] compiler_3.4.4 rstudioapi_0.11
[91] curl_4.3 interactiveDisplayBase_1.16.0
[93] ggsignif_0.6.0 tibble_3.0.3
[95] geneplotter_1.56.0 pcaPP_1.9-73
[97] stringi_1.4.6 lattice_0.20-38
[99] ProtGenerics_1.10.0 Matrix_1.2-18
[101] KMsurv_0.1-5 vctrs_0.3.1
[103] pillar_1.4.6 lifecycle_0.2.0
[105] BiocManager_1.30.10 data.table_1.12.8
[107] bitops_1.0-6 httpuv_1.5.2
[109] rtracklayer_1.38.3 qvalue_2.10.0
[111] R6_2.4.1 latticeExtra_0.6-28
[113] RMySQL_0.10.17 promises_1.1.0
[115] gridExtra_2.3 codetools_0.2-16
[117] lambda.r_1.2.4 MASS_7.3-51.4
[119] withr_2.2.0 GenomicAlignments_1.14.2
[121] Rsamtools_1.30.0 GenomeInfoDbData_1.0.0
[123] hms_0.5.2 rpart_4.1-15
[125] tidyr_1.1.0 rvcheck_0.1.7
[127] shiny_1.4.0 base64enc_0.1-3
Please modify the download count data from Gene Expression Omnibus and change the path in jupyter notebook, then run the code within R
The expected output was descripted in our article method section, and the output figure labels and colors could be further modified by Adobe Illustrator