Package: ISoLDE 1.40.0

Christelle Reynès

ISoLDE: Integrative Statistics of alleLe Dependent Expression

This package provides ISoLDE a new method for identifying imprinted genes. This method is dedicated to data arising from RNA sequencing technologies. The ISoLDE package implements original statistical methodology described in the publication below.

Authors:Christelle Reynès [aut, cre], Marine Rohmer [aut], Guilhem Kister [aut]

ISoLDE_1.40.0.tar.gz
ISoLDE_1.40.0.zip(r-4.7-x86_64)ISoLDE_1.40.0.zip(r-4.6-x86_64)ISoLDE_1.40.0.zip(r-4.5-x86_64)
ISoLDE_1.40.0.tgz(r-4.6-x86_64)ISoLDE_1.40.0.tgz(r-4.6-arm64)ISoLDE_1.40.0.tgz(r-4.5-x86_64)ISoLDE_1.40.0.tgz(r-4.5-arm64)
ISoLDE_1.40.0.tar.gz(r-4.7-arm64)ISoLDE_1.40.0.tar.gz(r-4.7-x86_64)ISoLDE_1.40.0.tar.gz(r-4.6-arm64)ISoLDE_1.40.0.tar.gz(r-4.6-x86_64)
ISoLDE_1.40.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ISoLDE/json (API)

# Install 'ISoLDE' in R:

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

Uses libs:

openmp– GCC OpenMP (GOMP) support library

Datasets:

filteredASRcounts - NORMALIZED AND FILTERED ALLELE SPECIFIC READ (ASR) COUNTS FOR AN EXPERIENCE WITH MORE THAN TWO REPLICATES
normASRcounts - NORMALIZED ALLELE SPECIFIC READ (ASR) COUNTS FOR AN EXPERIENCE WITH MORE THAN TWO REPLICATES
rawASRcounts - RAW ALLELE SPECIFIC READ (ASR) COUNTS FOR AN EXPERIENCE WITH MORE THAN TWO REPLICATES
target - METADATA ABOUT THE ASR COUNT DATA.

On BioConductor:ISoLDE-1.41.0(bioc 3.24)ISoLDE-1.40.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology geneexpression transcription genesetenrichment genetics sequencing rnaseq multiplecomparison snp geneticvariability epigenetics mathematicalbiology generegulation openmp

2.30 score 5 scripts 346 downloads 5 exports 0 dependencies

Last updated from:fe394f5424 (on RELEASE_3_23). Checks:12 WARNING, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	121
linux-devel-arm64	WARNING	249
linux-devel-x86_64	WARNING	265
source / vignettes	OK	168
linux-release-arm64	WARNING	126
linux-release-x86_64	WARNING	212
macos-release-arm64	WARNING	102
macos-release-x86_64	WARNING	194
macos-oldrel-arm64	WARNING	180
macos-oldrel-x86_64	WARNING	342
windows-devel-x86_64	WARNING	130
windows-release-x86_64	WARNING	143
windows-oldrel-x86_64	WARNING	122
wasm-release	OK	93

Exports:filterT isolde_test readNormInput readRawInput readTarget

Dependencies:

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
INTEGRATIVE STATISTICS OF ALLELE DEPENDENT EXPRESSION	ISoLDE-package ISoLDE
NORMALIZED AND FILTERED ALLELE SPECIFIC READ (ASR) COUNTS FOR AN EXPERIENCE WITH MORE THAN TWO REPLICATES	filteredASRcounts filteredASRcounts.rda
FILTERING GENES BEFORE STATISTICAL ANALYSIS	filterT
Statistical analysis of Allele specific read (ASR) counts	isolde_test
NORMALIZED ALLELE SPECIFIC READ (ASR) COUNTS FOR AN EXPERIENCE WITH MORE THAN TWO REPLICATES	normASRcounts normASRcounts_file normASRcounts_file.txt
RAW ALLELE SPECIFIC READ (ASR) COUNTS FOR AN EXPERIENCE WITH MORE THAN TWO REPLICATES	rawASRcounts rawASRcounts_file rawASRcounts_file.txt
READ THE NORMALIZED DATA FILE	readNormInput
READ THE RAW DATA FILE	readRawInput
READ THE TARGET FILE	readTarget
METADATA ABOUT THE ASR COUNT DATA.	target target_file target_file.txt