Package: GNOSIS 1.11.0

Lydia King

GNOSIS: Genomics explorer using statistical and survival analysis in R

GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities. These include data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research.

Authors:Lydia King [aut, cre], Marcel Ramos [ctb]

GNOSIS_1.11.0.tar.gz
GNOSIS_1.11.0.zip(r-4.7)GNOSIS_1.11.0.zip(r-4.6)GNOSIS_1.11.0.zip(r-4.5)
GNOSIS_1.11.0.tgz(r-4.6-any)GNOSIS_1.11.0.tgz(r-4.5-any)
GNOSIS_1.11.0.tar.gz(r-4.7-any)GNOSIS_1.11.0.tar.gz(r-4.6-any)
GNOSIS_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GNOSIS/json (API)

# Install 'GNOSIS' in R:

install.packages('GNOSIS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lydia-king/gnosis/issues

On BioConductor:GNOSIS-1.11.0(bioc 3.24)GNOSIS-1.10.0(bioc 3.23)

software shinyapps survival gui

4.85 score 7 stars 7 scripts 272 downloads 1 exports 300 dependencies

Last updated from:2f94c0859b. Checks:8 WARNING, 2 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	WARNING	290
linux-devel-x86_64	WARNING	531
source / vignettes	OK	408
linux-release-x86_64	WARNING	564
macos-release-arm64	WARNING	360
macos-oldrel-arm64	WARNING	245
windows-devel	WARNING	418
windows-release	WARNING	412
windows-oldrel	WARNING	444
wasm-release	OK	254

Exports:GNOSIS

Dependencies:abind AnnotationDbi AnVIL AnVILBase anytime askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bookdown boot broom bslib BWStest cachem callr car carData cBioPortalData cellranger chron cigarillo class cli clipr codetools colorspace commonmark compareGroups conflicted corrplot cowplot cpp11 crayon crosstalk curl dashboardthemes data.table DBI dbplyr DelayedArray Deriv DescTools digest DNAcopy doBy dplyr DT dtplyr e1071 evaluate Exact exactRankTests expm fabricatr farver fastmap filelock flextable fontawesome fontBitstreamVera fontLiberation fontquiver forcats foreach forecast formatR Formula fracdiff fresh fs futile.logger futile.options future future.apply gargle GCPtools gdtools generics GenomeInfoDb GenomicAlignments GenomicDataCommons GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif ggtext gld glmnet globals glue gmp googledrive googlesheets4 gridExtra gridtext gtable HardyWeinberg haven highr hms htmltools htmlwidgets httpuv httr httr2 ids inum IRanges isoband iterators jomo jpeg jquerylib jsonlite kableExtra KEGGREST keyring knitr kSamples labeling lambda.r later lattice lazyeval libcoin lifecycle listenv litedown lme4 lmom lmtest lubridate maftools magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats maxstat memoise mgcv mice mime miniUI minqa mitml modelr multcompView MultiAssayExperiment mvtnorm nanotime nlme nloptr nnet numDeriv officer openssl operator.tools ordinal otel pan parallelly partykit pbkrtest pheatmap pillar pkgconfig plyr PMCMRplus png polynom prettyunits processx progress promises proxy ps purrr quantreg R.cache R.methodsS3 R.oo R.utils R6 ragg RaggedExperiment rapiclient rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppCCTZ RcppDate RcppEigen RCurl Rdpack readr readxl reformulas rematch rematch2 reprex reshape2 restfulr Rhtslib rjson RJSONIO rlang rmarkdown rmdformats Rmpfr rootSolve rpart rprojroot Rsamtools Rsolnp RSQLite rstatix rstudioapi RTCGAToolbox rtracklayer rvest S4Arrays S4Vectors S7 sass scales selectr Seqinfo shape shiny shinycssloaders shinydashboard shinydashboardPlus shinyjs shinylogs shinymeta shinyWidgets snow sourcetools SparseArray SparseM stringi stringr styler SummarizedExperiment SuppDists survival survminer svglite sys systemfonts TCGAutils textshaping tibble tidyr tidyselect tidyverse timechange timeDate tinytex truncnorm tzdb ucminf UCSC.utils urca utf8 uuid vctrs viridisLite vroom waiter withr writexl xfun XML xml2 xtable XVector yaml zip zoo

GNOSIS: Genomics explorer using statistical and survival analysis in R

Introduction | Installation | Loading the package | Launching GNOSIS | GNOSIS layout | Data upload and preview | Data reformatting and filtering | Data visualisation | Statistical and survival analysis | Mutation Analysis | Input Log | Additional Resources | Session Info

Rendered fromGNOSIS.Rmdusingknitr::rmarkdown

Last update: 2023-10-14
Started: 2023-09-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
#' Initialise GNOSIS	GNOSIS

Usage by other packages (reverse dependencies)