Package: vidger 1.27.0

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]

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vidger.pdf |vidger.html✨
vidger/json (API)
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# 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-1.27.0(bioc 3.21)vidger-1.26.0(bioc 3.20)

immunooncology visualization rnaseq differentialexpression geneexpression data-munging differential-expression gene-expression rna-seq-analysis

6.59 score 18 stars 27 scripts 270 downloads 2 mentions 9 exports 104 dependencies

Last updated 23 days agofrom:030cd02288. Checks:OK: 4 WARNING: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	OK	Oct 31 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	WARNING	Oct 31 2024
R-4.3-mac	OK	Oct 31 2024

Exports:vsBoxPlot vsDEGMatrix vsFourWay vsMAMatrix vsMAPlot vsScatterMatrix vsScatterPlot vsVolcano vsVolcanoMatrix

Dependencies:abind askpass base64enc BH Biobase BiocGenerics BiocParallel bslib cachem cli 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 highr hms htmltools httr IRanges isoband jquerylib jsonlite knitr labeling 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 rlang rmarkdown S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml zlibbioc

ViDGER Supplementary Material

Brandon Monier, Adam McDermaid, Jing Zhao, Qin Ma

Rendered fromvidger.Rmdusingknitr::rmarkdownon Oct 31 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