Contact: Aspen Coyle, afcoyle@uw.edu Roberts Lab, UW-SAFS
Last edited README: 2021-03-04
Examining differential expression of shared Hematodinium/C. bairdi libraries over temperature and time.
All libraries originate from Grace Crandall's research. The same libraries and general notation is used here.
Windows 10, x64 (OS build: 18363.1256)
Running WSL version 1
R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils datasets methods
[10] base
other attached packages:
[1] VennDiagram_1.6.20 futile.logger_1.4.3 ape_5.4-1
[4] vsn_3.58.0 forcats_0.5.1 stringr_1.4.0
[7] dplyr_1.0.4 purrr_0.3.4 readr_1.4.0
[10] tidyr_1.1.3 tibble_3.1.0 ggplot2_3.3.3
[13] tidyverse_1.3.0 DESeq2_1.30.1 SummarizedExperiment_1.20.0
[16] Biobase_2.50.0 MatrixGenerics_1.2.1 matrixStats_0.58.0
[19] GenomicRanges_1.42.0 GenomeInfoDb_1.26.2 IRanges_2.24.1
[22] S4Vectors_0.28.1 BiocGenerics_0.36.0 apeglm_1.12.0
data: unmodified data files
graphs: output from various R packages ran as part of analyses. Does include several tables
output: output from analyses
paper: publication
scripts: code to run analyses. Does include some output within the GO-MWU directory, as it is required for GO-MWU to run.
Many folders in output/ and graphs/ are split into subdirectories labeled cbaihemat_transcriptomev2.0 and hemat_transcriptomev1.6. These correspond to analyses performed using cbai_transcriptomev2.0 and hemat_transcriptomev1.6