Last updated: 2022-07-13
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Knit directory:
20180328_Atkins_RatFracture/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | fb03c6a | steveped | 2022-07-13 | Tidied description of rats |
| html | fcfd11c | Steve Pederson | 2022-07-07 | Build site. |
| Rmd | c4a6c6c | Steve Pederson | 2022-07-06 | Reanalysed using voom |
| Rmd | dd28879 | Steve Pederson | 2022-07-06 | Setup initial DGE after restructure |
| html | dd28879 | Steve Pederson | 2022-07-06 | Setup initial DGE after restructure |
| Rmd | 1ad8b01 | Steve Pederson | 2022-07-05 | Start workflowr project. |
knitr::opts_chunk$set(
message = FALSE, warning = FALSE,
fig.height = 8, fig.width = 10
)library(tidyverse)
library(pander)suffix <- "_L001_R1.fastq.gz"
samples <- read_csv(
here::here("data/targets.csv")
) %>%
mutate(File = paste0(File, suffix))This is a simple analysis of Single-End, Total RNA-Seq data associated with bone fractures in the Zucker Diabetic Fatty (ZDF) rat model. Samples are as follows.
pander(
samples,
justify = "lll",
caption = "Samples included for RNA-Seq analysis."
)| Rat | group | File |
|---|---|---|
| 179_F | Diabetic | 179_F_CB2YGANXX_ATCACG_L001_R1.fastq.gz |
| 187_F | Diabetic | 187_F_CB2YGANXX_CGATGT_L001_R1.fastq.gz |
| 188_F | Diabetic | 188_F_CB2YGANXX_TTAGGC_L001_R1.fastq.gz |
| 190_F | Control | 190_F_CB2YGANXX_TGACCA_L001_R1.fastq.gz |
| 192_F | Control | 192_F_CB2YGANXX_ACAGTG_L001_R1.fastq.gz |
| 194_F | Control | 194_F_CB2YGANXX_GCCAAT_L001_R1.fastq.gz |
The primary workflow is to trim the data, then align and count reads
in a gene-specific manner. The genome build used was
Rnor_6.0 with gene annotations derived from Ensembl Release
96.
Tool versions used were:
sessionInfo()R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pander_0.6.5 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.9
[5] purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.7
[9] ggplot2_3.3.6 tidyverse_1.3.1 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 here_1.0.1 lubridate_1.8.0 getPass_0.2-2
[5] ps_1.7.1 assertthat_0.2.1 rprojroot_2.0.3 digest_0.6.29
[9] utf8_1.2.2 R6_2.5.1 cellranger_1.1.0 backports_1.4.1
[13] reprex_2.0.1 evaluate_0.15 httr_1.4.3 pillar_1.7.0
[17] rlang_1.0.4 readxl_1.4.0 rstudioapi_0.13 whisker_0.4
[21] callr_3.7.0 jquerylib_0.1.4 rmarkdown_2.14 bit_4.0.4
[25] munsell_0.5.0 broom_1.0.0 compiler_4.2.1 httpuv_1.6.5
[29] modelr_0.1.8 xfun_0.31 pkgconfig_2.0.3 htmltools_0.5.2
[33] tidyselect_1.1.2 fansi_1.0.3 withr_2.5.0 crayon_1.5.1
[37] tzdb_0.3.0 dbplyr_2.2.1 later_1.3.0 grid_4.2.1
[41] jsonlite_1.8.0 gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.3
[45] git2r_0.30.1 magrittr_2.0.3 scales_1.2.0 vroom_1.5.7
[49] cli_3.3.0 stringi_1.7.8 fs_1.5.2 promises_1.2.0.1
[53] xml2_1.3.3 bslib_0.3.1 ellipsis_0.3.2 generics_0.1.3
[57] vctrs_0.4.1 tools_4.2.1 bit64_4.0.5 glue_1.6.2
[61] hms_1.1.1 parallel_4.2.1 processx_3.7.0 fastmap_1.1.0
[65] yaml_2.3.5 colorspace_2.0-3 rvest_1.0.2 knitr_1.39
[69] haven_2.5.0 sass_0.4.1