Package: phantasusLite 1.11.4

Alexey Sergushichev

phantasusLite: Loading and annotation RNA-seq counts matrices

PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.

Authors:Rita Sablina [aut], Maxim Kleverov [aut], Alexey Sergushichev [aut, cre]

phantasusLite_1.11.4.tar.gz
phantasusLite_1.11.4.zip(r-4.7)phantasusLite_1.11.4.zip(r-4.6)phantasusLite_1.11.4.zip(r-4.5)
phantasusLite_1.11.4.tgz(r-4.6-any)phantasusLite_1.11.4.tgz(r-4.5-any)
phantasusLite_1.11.4.tar.gz(r-4.7-any)phantasusLite_1.11.4.tar.gz(r-4.6-any)
phantasusLite_1.11.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phantasusLite/json (API)

# Install 'phantasusLite' in R:

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

Bug tracker:https://github.com/alserglab/phantasuslite/issues

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

geneexpression transcriptomics rnaseq

6.00 score 11 stars 1 packages 9 scripts 6 exports 33 dependencies

Last updated from:6c4a67c9b2. Checks:4 NOTE, 4 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	162
linux-devel-x86_64	ERROR	350
source / vignettes	OK	257
linux-release-x86_64	NOTE	330
macos-release-arm64	ERROR	193
macos-oldrel-arm64	NOTE	212
windows-devel	ERROR	248
windows-release	ERROR	220
windows-oldrel	NOTE	204
wasm-release	OK	131

Exports:getHSDSFileList inferCondition loadCountsFromH5FileHSDS loadCountsFromHSDS readGct writeGct

Dependencies:abind askpass Biobase BiocGenerics cli curl data.table DelayedArray generics glue httr IRanges jsonlite lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl R6 rhdf5client rjson rlang S4Arrays S4Vectors SparseArray stringi stringr sys vctrs XVector

phantasusLite tutorial

Rendered fromphantasusLite-tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-06-18
Started: 2023-09-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Returns list of all HDF5-files on HSDS-server	getHSDSFileList
Adds condition to the annotation.	inferCondition
Load count matrix from remote HDF5-file	loadCountsFromH5FileHSDS
Load count matrix from HDF5-files.	loadCountsFromHSDS
Reads ExpressionSet from a GCT file.	readGct
Saves ExpressionSet to a GCT file (version 1.3).	writeGct