postNet
This is the development version of postNet; to use it, please install the devel version of Bioconductor.
Post-transcriptional network modeling
Bioconductor version: Development (3.23)
A tool that enables in silico identification, integration, and modeling of mRNA features that influence post-transcriptional regulation of gene expression at a transcriptome-wide scale.
Author: Krzysztof Szkop [aut, cre], Kathleen Watt [aut], Ola Larsson [aut]
Maintainer: Krzysztof Szkop <krzysztof.szkop at gmail.com>
citation("postNet")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("postNet")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("postNet")| Post-transcriptional network modelling with postNet | HTML | R Script |
| Reference Manual |
Details
| biocViews | Annotation, FeatureExtraction, GeneExpression, GeneRegulation, Network, RNASeq, RiboSeq, Sequencing, Software, Transcriptomics |
| Version | 0.99.8 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | dplyr, plyr, Biostrings, data.table, gridExtra, seqinr, R.utils, reshape2, vioplot, stringr, plotrix, gplots, ggplot2, ggrepel, anota2seq, memes, GenomicRanges, IRanges, WriteXLS, randomForest, igraph, Boruta, ROCR, caret, msigdb, ExperimentHub, AnnotationHub, GSEABase, fgsea, org.Hs.eg.db, org.Mm.eg.db, RColorBrewer, httr2, rvest, umap, clusterProfiler(>= 4.18.4), gage, withr, grDevices, graphics, methods, stats, utils, tools, BiocFileCache, curl |
| System Requirements | |
| URL | https://github.com/kszkop/postNet |
| Bug Reports | https://github.com/kszkop/postNet/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, pdftools, magick, testthat (>= 3.0.0) |
| Linking To | Rcpp, BH |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | postNet_0.99.8.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | postNet_0.99.8.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/postNet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/postNet |
| Bioc Package Browser | https://code.bioconductor.org/browse/postNet/ |
| Package Short Url | https://bioconductor.org/packages/postNet/ |
| Package Downloads Report | Download Stats |