TrendCatcher is an open source R-package that allows users to systematically analyze and visualize time course data. Please cite "Temporal transcriptomic analysis using TrendCatcher identifies early and persistent neutrophil activation in severe COVID-19" by Xinge Wang et al published in JCI Insight (2022) - https://insight.jci.org/articles/view/157255
Have issues installing TrendCatcher on Macbook Pro (see below)
if (!require("devtools")) {
install.packages("devtools")
}
devtools::install_github("jaleesr/TrendCatcher", dependencies = TRUE, build_vignettes = FALSE)
Downloading GitHub repo jaleesr/TrendCatcher@HEAD
Skipping 8 packages not available: biomaRt, org.Mm.eg.db, org.Hs.eg.db, edgeR, clusterProfiler, DESeq2, ComplexHeatmap, sva
── R CMD build ──────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/p2/dz3xnjxx3ql7vs6jm0fhsxwh0000gn/T/RtmpTcMeHd/remotes242c132ffd8f/jaleesr-TrendCatcher-035793a/DESCRIPTION’ (351ms)
─ preparing ‘TrendCatcher’: (2s)
✔ checking DESCRIPTION meta-information
─ checking for LF line-endings in source and make files and shell scripts (569ms)
─ checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘TrendCatcher/inst/extdata/BrainMasterList.rda’
‘TrendCatcher/inst/extdata/BrainMasterList_Symbol.rda’
‘TrendCatcher/inst/extdata/Brain_TimeHeatmap.rda’
‘TrendCatcher/inst/extdata/MasterListModerate.rda’
‘TrendCatcher/inst/extdata/MasterListSevere.rda’
‘TrendCatcher/inst/extdata/htSevere.rda’
─ building ‘TrendCatcher_1.0.0.tar.gz’
ERROR: dependencies ‘sva’, ‘ComplexHeatmap’, ‘clusterProfiler’, ‘edgeR’, ‘org.Hs.eg.db’, ‘org.Mm.eg.db’ are not available for package ‘TrendCatcher’
removing ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/TrendCatcher’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/p2/dz3xnjxx3ql7vs6jm0fhsxwh0000gn/T//RtmpTcMeHd/file242c33afc120/TrendCatcher_1.0.0.tar.gz’ had non-zero exit status
install.packages("/Users/bilal/R/iPSC/TrendCatcher_1.0.0.tar.gz", repos = NULL, type = "source")
ERROR: dependencies ‘sva’, ‘ComplexHeatmap’, ‘clusterProfiler’, ‘edgeR’, ‘org.Hs.eg.db’, ‘org.Mm.eg.db’ are not available for package ‘TrendCatcher’
removing ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/TrendCatcher’
Warning in install.packages :
installation of package ‘/Users/bilal/R/iPSC/TrendCatcher_1.0.0.tar.gz’ had non-zero exit status
session_info()
─ Session info ────────────────────────────────────────────────────────────────────────
setting value
version R version 4.4.0 (2024-04-24)
os macOS Big Sur 11.7.10
system x86_64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/London
date 2024-05-03
rstudio 2024.04.0+735 Chocolate Cosmos (desktop)
pandoc NA
Have issues installing TrendCatcher on Macbook Pro (see below)
ERROR: dependencies ‘sva’, ‘ComplexHeatmap’, ‘clusterProfiler’, ‘edgeR’, ‘org.Hs.eg.db’, ‘org.Mm.eg.db’ are not available for package ‘TrendCatcher’
─ Packages ──────────────────────────────────────────────────────────────────────────── package version date (UTC) lib source cachem 1.0.8 2023-05-01 [1] CRAN (R 4.4.0) callr 3.7.6 2024-03-25 [1] CRAN (R 4.4.0) cli 3.6.2 2023-12-11 [1] CRAN (R 4.4.0) curl 5.2.1 2024-03-01 [1] CRAN (R 4.4.0) desc 1.4.3 2023-12-10 [1] CRAN (R 4.4.0) devtools 2.4.5 2022-10-11 [1] CRAN (R 4.4.0) digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.0) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.4.0) fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.4.0) fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0) glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0) htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0) htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0) httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.0) later 1.3.2 2023-12-06 [1] CRAN (R 4.4.0) lattice 0.22-6 2024-03-20 [1] CRAN (R 4.4.0) lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.0) mime 0.12 2021-09-28 [1] CRAN (R 4.4.0) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.0) nlme 3.1-164 2023-11-27 [1] CRAN (R 4.4.0) pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.4.0) pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.4.0) processx 3.8.4 2024-03-16 [1] CRAN (R 4.4.0) profvis 0.3.8 2023-05-02 [1] CRAN (R 4.4.0) promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.0) ps 1.7.6 2024-01-18 [1] CRAN (R 4.4.0) purrr 1.0.2 2023-08-10 [1] CRAN (R 4.4.0) R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0) Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.4.0) remotes 2.5.0 2024-03-17 [1] CRAN (R 4.4.0) rlang 1.1.3 2024-01-10 [1] CRAN (R 4.4.0) rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0) shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.4.0) stringi 1.8.3 2023-12-11 [1] CRAN (R 4.4.0) stringr 1.5.1 2023-11-14 [1] CRAN (R 4.4.0) urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.4.0) usethis * 2.2.3 2024-02-19 [1] CRAN (R 4.4.0) vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.0)
[1] /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library