Package: vidger 1.25.0

Brandon Monier

vidger: Create rapid visualizations of RNAseq data in R

The aim of vidger is to rapidly generate information-rich visualizations for the interpretation of differential gene expression results from three widely-used tools: Cuffdiff, DESeq2, and edgeR.

Authors:Brandon Monier [aut, cre], Adam McDermaid [aut], Jing Zhao [aut], Qin Ma [aut, fnd]

vidger_1.25.0.tar.gz
vidger_1.25.0.zip(r-4.5)vidger_1.25.0.zip(r-4.4)vidger_1.25.0.zip(r-4.3)
vidger_1.25.0.tgz(r-4.4-any)vidger_1.25.0.tgz(r-4.3-any)
vidger_1.25.0.tar.gz(r-4.5-noble)vidger_1.25.0.tar.gz(r-4.4-noble)
vidger_1.25.0.tgz(r-4.4-emscripten)vidger_1.25.0.tgz(r-4.3-emscripten)
vidger.pdf |vidger.html✨
vidger/json (API)
NEWS

# Install 'vidger' in R:

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

Bug tracker:https://github.com/btmonier/vidger/issues

Datasets:

df.cuff - A 'cuffdiff' example dataset
df.deseq - A 'DESeq2' example dataset
df.edger - A 'edgeR' example dataset

On BioConductor:vidger-1.25.0(bioc 3.20)vidger-1.24.0(bioc 3.19)

bioconductor-package

9 exports 0.91 score 115 dependencies 2 mentions

Last updated 2 months agofrom:4230b76ff7

Exports:vsBoxPlot vsDEGMatrix vsFourWay vsMAMatrix vsMAPlot vsScatterMatrix vsScatterPlot vsVolcano vsVolcanoMatrix

Dependencies:abind askpass backports base64enc BH Biobase BiocGenerics BiocParallel bit bit64 broom broom.helpers bslib cachem cli clipr codetools colorspace cpp11 crayon curl DelayedArray DESeq2 digest dplyr edgeR evaluate fansi farver fastmap fontawesome forcats formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges GGally ggplot2 ggrepel ggstats glue gtable haven highr hms htmltools httr IRanges isoband jquerylib jsonlite knitr labeling labelled lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl patchwork pillar pkgconfig plyr prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo readr rlang rmarkdown S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XVector yaml zlibbioc

ViDGER Supplementary Material

Brandon Monier, Adam McDermaid, Jing Zhao, Qin Ma

Rendered fromvidger.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2019-07-15
Started: 2018-02-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A `cuffdiff` example dataset	df.cuff
A `DESeq2` example dataset	df.deseq
A `edgeR` example dataset	df.edger
Box plot for log_{10}(FPKM or CPM) distributions	vsBoxPlot
Differential gene expression matrix	vsDEGMatrix
Four-Way plot for comparison of log fold changes in a multiple factor RNA-seq experiment from different analytical objects	vsFourWay
MA plot matrix from log_{2} fold changes and -log_{10}(p-values)	vsMAMatrix
MA plot from mean expression and log fold changes from different analytical objects	vsMAPlot
Scatter plot matrix of log_{10}(FPKM or CPM) values	vsScatterMatrix
Scatter plot of log_{10}(FPKM or CPM) values	vsScatterPlot
Volcano plot from log_{2} fold changes and -log_{10}(p-values)	vsVolcano
Volcano plot matrix from log_{2} fold changes and -log_{10}(p-values)	vsVolcanoMatrix