Package: ISoLDE 1.35.0

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_1.35.0.tar.gz
ISoLDE_1.35.0.zip(r-4.5)ISoLDE_1.35.0.zip(r-4.4)ISoLDE_1.35.0.zip(r-4.3)
ISoLDE_1.35.0.tgz(r-4.4-x86_64)ISoLDE_1.35.0.tgz(r-4.4-arm64)ISoLDE_1.35.0.tgz(r-4.3-x86_64)ISoLDE_1.35.0.tgz(r-4.3-arm64)
ISoLDE_1.35.0.tar.gz(r-4.5-noble)ISoLDE_1.35.0.tar.gz(r-4.4-noble)
ISoLDE_1.35.0.tgz(r-4.4-emscripten)ISoLDE_1.35.0.tgz(r-4.3-emscripten)
ISoLDE.pdf |ISoLDE.html✨
ISoLDE/json (API)
NEWS

# Install 'ISoLDE' in R:

install.packages('ISoLDE', repos = c('https://bioc.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-1.35.0(bioc 3.21)ISoLDE-1.34.0(bioc 3.20)

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 2 scripts 140 downloads 5 exports 0 dependencies

Last updated 2 months agofrom:e892789d33. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win-x86_64	WARNING	Nov 29 2024
R-4.5-linux-x86_64	WARNING	Nov 29 2024
R-4.4-win-x86_64	WARNING	Nov 29 2024
R-4.4-mac-x86_64	WARNING	Nov 29 2024
R-4.4-mac-aarch64	WARNING	Nov 29 2024
R-4.3-win-x86_64	WARNING	Nov 29 2024
R-4.3-mac-x86_64	WARNING	Nov 29 2024
R-4.3-mac-aarch64	WARNING	Nov 29 2024

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