https://github.com/likelet/scrcgenomics
Sourcecode for SCRC project.
https://github.com/likelet/scrcgenomics
Last synced: 3 months ago
JSON representation
Sourcecode for SCRC project.
- Host: GitHub
- URL: https://github.com/likelet/scrcgenomics
- Owner: likelet
- Created: 2023-07-07T07:21:44.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2023-07-13T13:11:20.000Z (almost 2 years ago)
- Last Synced: 2025-01-07T20:45:53.506Z (4 months ago)
- Language: R
- Size: 65 MB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# SCRCgenomics
Sourcecode for SCRC project.
# R session info
``` r
sessioninfo::session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23)
os Ubuntu 20.04.6 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2023-07-08
rstudio 2022.07.2+576 Spotted Wakerobin (server)
pandoc 2.19.2 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/ (via rmarkdown)
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] RSPM (R 4.2.0)
assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.2.0)
backports 1.4.1 2021-12-13 [1] RSPM (R 4.2.0)
Biobase * 2.58.0 2022-11-01 [1] Bioconductor
BiocGenerics * 0.44.0 2022-11-01 [1] Bioconductor
BiocIO 1.8.0 2022-11-01 [1] Bioconductor
BiocParallel 1.32.6 2023-03-17 [1] Bioconductor
Biostrings * 2.66.0 2022-11-01 [1] Bioconductor
bitops 1.0-7 2021-04-24 [1] RSPM (R 4.2.0)
boot 1.3-28 2021-05-03 [4] CRAN (R 4.2.1)
broom 1.0.1 2022-08-29 [1] RSPM (R 4.2.0)
broom.helpers 1.9.0 2022-09-23 [1] RSPM (R 4.2.0)
BSgenome * 1.66.3 2023-02-16 [1] Bioconductor
BSgenome.Hsapiens.UCSC.hg19 * 1.4.3 2023-05-09 [1] Bioconductor
car 3.1-1 2022-10-19 [1] RSPM (R 4.2.0)
carData 3.0-5 2022-01-06 [1] RSPM (R 4.2.0)
circlize 0.4.15 2022-05-10 [1] RSPM (R 4.2.0)
cli 3.4.1 2022-09-23 [1] RSPM (R 4.2.0)
clue 0.3-62 2022-10-18 [1] RSPM (R 4.2.0)
cluster * 2.1.3 2022-03-28 [4] CRAN (R 4.2.1)
codetools 0.2-18 2020-11-04 [4] CRAN (R 4.2.1)
colorspace 2.0-3 2022-02-21 [1] RSPM (R 4.2.0)
ComplexHeatmap * 2.14.0 2022-11-01 [1] Bioconductor
cowplot * 1.1.1 2020-12-30 [1] RSPM (R 4.2.0)
crayon 1.5.2 2022-09-29 [1] RSPM (R 4.2.0)
data.table * 1.14.4 2022-10-17 [1] RSPM (R 4.2.0)
DBI 1.1.3 2022-06-18 [1] RSPM (R 4.2.0)
DelayedArray 0.24.0 2022-11-01 [1] Bioconductor
digest 0.6.30 2022-10-18 [1] RSPM (R 4.2.0)
doParallel * 1.0.17 2022-02-07 [1] RSPM (R 4.2.0)
dplyr * 1.0.10 2022-09-01 [1] RSPM (R 4.2.0)
ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.2.0)
evaluate 0.17 2022-10-07 [1] RSPM (R 4.2.0)
fansi 1.0.3 2022-03-24 [1] RSPM (R 4.2.0)
fastmap 1.1.0 2021-01-25 [1] RSPM (R 4.2.0)
finalfit * 1.0.5 2022-08-09 [1] RSPM (R 4.2.0)
forcats 0.5.2 2022-08-19 [1] RSPM (R 4.2.0)
foreach * 1.5.2 2022-02-02 [1] RSPM (R 4.2.0)
formatR 1.12 2022-03-31 [1] RSPM (R 4.2.0)
Formula 1.2-4 2020-10-16 [1] RSPM (R 4.2.0)
futile.logger * 1.4.3 2016-07-10 [1] RSPM (R 4.2.0)
futile.options 1.0.1 2018-04-20 [1] RSPM (R 4.2.0)
generics 0.1.3 2022-07-05 [1] RSPM (R 4.2.0)
GenomeInfoDb * 1.34.9 2023-02-02 [1] Bioconductor
GenomeInfoDbData 1.2.9 2023-05-16 [1] Bioconductor
GenomicAlignments 1.34.1 2023-03-09 [1] Bioconductor
GenomicRanges * 1.50.2 2022-12-16 [1] Bioconductor
GetoptLong 1.0.5 2020-12-15 [1] RSPM (R 4.0.3)
gg.gap * 1.3 2019-09-30 [1] RSPM (R 4.0.0)
ggalluvial 0.12.3 2020-12-05 [1] RSPM (R 4.0.3)
ggplot2 * 3.3.6 2022-05-03 [1] RSPM (R 4.2.0)
ggpubr * 0.4.0 2020-06-27 [1] RSPM (R 4.2.0)
ggrepel * 0.9.1 2021-01-15 [1] RSPM (R 4.2.0)
ggsci * 2.9 2018-05-14 [1] RSPM (R 4.2.0)
ggsignif 0.6.4 2022-10-13 [1] RSPM (R 4.2.0)
ggthemr * 1.1.0 2021-12-14 [2] Github (cttobin/ggthemr@4a31e0d)
GlobalOptions 0.1.2 2020-06-10 [1] RSPM (R 4.0.3)
glue 1.6.2 2022-02-24 [1] RSPM (R 4.2.0)
gridBase 0.4-7 2014-02-24 [1] RSPM (R 4.0.3)
gridExtra * 2.3 2017-09-09 [1] RSPM (R 4.2.0)
gt 0.7.0 2022-08-25 [1] RSPM (R 4.2.0)
gtable 0.3.1 2022-09-01 [1] RSPM (R 4.2.0)
gtsummary * 1.6.2 2022-09-30 [1] RSPM (R 4.2.0)
hms 1.1.2 2022-08-19 [1] RSPM (R 4.2.0)
htmltools * 0.5.3 2022-07-18 [1] RSPM (R 4.2.0)
httr 1.4.4 2022-08-17 [1] RSPM (R 4.2.0)
IRanges * 2.32.0 2022-11-01 [1] Bioconductor
iterators * 1.0.14 2022-02-05 [1] RSPM (R 4.2.0)
kableExtra 1.3.4 2021-02-20 [1] RSPM (R 4.2.0)
km.ci 0.5-2 2009-08-30 [2] RSPM (R 4.0.3)
KMsurv 0.1-5 2012-12-03 [2] RSPM (R 4.0.3)
knitr 1.40 2022-08-24 [1] RSPM (R 4.2.0)
lambda.r 1.2.4 2019-09-18 [1] RSPM (R 4.2.0)
lattice * 0.20-45 2021-09-22 [4] CRAN (R 4.2.1)
lifecycle 1.0.3 2022-10-07 [1] RSPM (R 4.2.0)
lpSolve 5.6.17 2022-10-10 [1] RSPM (R 4.2.0)
maftools * 2.6.05 2021-02-04 [2] Bioconductor
magrittr * 2.0.3 2022-03-30 [1] RSPM (R 4.2.0)
MASS 7.3-57 2022-04-22 [4] CRAN (R 4.2.1)
Matrix 1.5-1 2022-09-13 [1] RSPM (R 4.2.0)
MatrixGenerics 1.10.0 2022-11-01 [1] Bioconductor
matrixStats 0.62.0 2022-04-19 [1] RSPM (R 4.2.0)
mice 3.14.0 2021-11-24 [1] RSPM (R 4.2.0)
munsell 0.5.0 2018-06-12 [1] RSPM (R 4.2.0)
MutationalPatterns * 3.8.1 2023-01-26 [3] Bioconductor
neutralitytestr * 0.0.3 2021-02-16 [1] RSPM (R 4.0.3)
NMF * 0.24.0 2022-03-29 [1] RSPM (R 4.2.1)
pheatmap * 1.0.12 2019-01-04 [1] RSPM (R 4.2.0)
pillar 1.8.1 2022-08-19 [1] RSPM (R 4.2.0)
pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.2.0)
pkgmaker * 0.32.2 2020-10-20 [1] RSPM (R 4.0.3)
plyr * 1.8.7 2022-03-24 [1] RSPM (R 4.2.0)
png 0.1-7 2013-12-03 [1] RSPM (R 4.2.0)
pracma 2.4.2 2022-09-22 [1] RSPM (R 4.2.0)
purrr 0.3.5 2022-10-06 [1] RSPM (R 4.2.0)
R6 2.5.1 2021-08-19 [1] RSPM (R 4.2.0)
RColorBrewer * 1.1-3 2022-04-03 [1] RSPM (R 4.2.0)
Rcpp 1.0.9 2022-07-08 [1] RSPM (R 4.2.0)
RCurl 1.98-1.9 2022-10-03 [1] RSPM (R 4.2.0)
readr 2.1.3 2022-10-01 [1] RSPM (R 4.2.0)
registry * 0.5-1 2019-03-05 [1] RSPM (R 4.0.0)
reshape2 * 1.4.4 2020-04-09 [1] RSPM (R 4.2.0)
restfulr 0.0.15 2022-06-16 [1] RSPM (R 4.2.1)
rjson 0.2.21 2022-01-09 [1] RSPM (R 4.2.0)
rlang 1.0.6 2022-09-24 [1] RSPM (R 4.2.0)
rmarkdown 2.17 2022-10-07 [1] RSPM (R 4.2.0)
Rmisc * 1.5.1 2022-05-02 [1] RSPM (R 4.2.0)
rngtools * 1.5.2 2021-09-20 [1] RSPM (R 4.2.0)
Rsamtools 2.14.0 2022-11-01 [1] Bioconductor
rstatix 0.7.0 2021-02-13 [1] RSPM (R 4.2.0)
rstudioapi 0.14 2022-08-22 [1] RSPM (R 4.2.0)
rtracklayer * 1.58.0 2022-11-01 [1] Bioconductor
rvest 1.0.3 2022-08-19 [1] RSPM (R 4.2.0)
S4Vectors * 0.36.2 2023-02-26 [1] Bioconductor
sampling * 2.9 2021-01-13 [1] RSPM (R 4.0.3)
scales * 1.2.1 2022-08-20 [1] RSPM (R 4.2.0)
sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.2.0)
shape 1.4.6 2021-05-19 [1] RSPM (R 4.2.0)
stringi 1.7.8 2022-07-11 [1] RSPM (R 4.2.0)
stringr 1.4.1 2022-08-20 [1] RSPM (R 4.2.0)
SummarizedExperiment 1.28.0 2022-11-01 [1] Bioconductor
survival * 3.3-1 2022-03-03 [4] CRAN (R 4.2.1)
survminer * 0.4.9 2021-03-09 [2] RSPM (R 4.0.3)
survMisc 0.5.5 2018-07-05 [2] RSPM (R 4.0.3)
svglite 2.0.0 2021-02-20 [2] RSPM (R 4.0.4)
systemfonts 1.0.4 2022-02-11 [1] RSPM (R 4.2.0)
table1 * 1.4.2 2021-06-06 [1] RSPM (R 4.2.0)
tibble 3.1.8 2022-07-22 [1] RSPM (R 4.2.0)
tidyr * 1.2.1 2022-09-08 [1] RSPM (R 4.2.0)
tidyselect 1.2.0 2022-10-10 [1] RSPM (R 4.2.0)
tzdb 0.3.0 2022-03-28 [1] RSPM (R 4.2.0)
utf8 1.2.2 2021-07-24 [1] RSPM (R 4.2.0)
vctrs 0.5.0 2022-10-22 [1] RSPM (R 4.2.0)
VennDiagram * 1.6.20 2018-03-28 [2] RSPM (R 4.0.0)
viridisLite 0.4.1 2022-08-22 [1] RSPM (R 4.2.0)
webshot 0.5.2 2019-11-22 [2] RSPM (R 4.0.3)
wesanderson * 0.3.6 2018-04-20 [1] RSPM (R 4.0.0)
withr 2.5.0 2022-03-03 [1] RSPM (R 4.2.0)
xfun 0.34 2022-10-18 [1] RSPM (R 4.2.0)
XML 3.99-0.11 2022-10-03 [1] RSPM (R 4.2.0)
xml2 1.3.3 2021-11-30 [1] RSPM (R 4.2.0)
xtable 1.8-4 2019-04-21 [1] RSPM (R 4.2.0)
XVector * 0.38.0 2022-11-01 [1] Bioconductor
yaml 2.3.6 2022-10-18 [1] RSPM (R 4.2.0)
zlibbioc 1.44.0 2022-11-01 [1] Bioconductor
zoo 1.8-11 2022-09-17 [1] RSPM (R 4.2.0)
```