Package: GRIN2 2.0.0

GRIN2: Genomic Random Interval (GRIN)

Improved version of 'GRIN' software that streamlines its use in practice to analyze genomic lesion data, accelerate its computing, and expand its analysis capabilities to answer additional scientific questions including a rigorous evaluation of the association of genomic lesions with RNA expression. Pounds, Stan, et al. (2013) <doi:10.1093/bioinformatics/btt372>.

Authors:Abdelrahman Elsayed [aut, cre, cph], Xueyuan Cao [aut], Lakshmi Anuhya patibandla [aut], Stanley Pounds [aut, cph]

GRIN2_2.0.0.tar.gz
GRIN2_2.0.0.zip(r-4.7)GRIN2_2.0.0.zip(r-4.6)GRIN2_2.0.0.zip(r-4.5)
GRIN2_2.0.0.tgz(r-4.6-any)GRIN2_2.0.0.tgz(r-4.5-any)
GRIN2_2.0.0.tar.gz(r-4.7-any)GRIN2_2.0.0.tar.gz(r-4.6-any)
GRIN2_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GRIN2/json (API)

# Install 'GRIN2' in R:
install.packages('GRIN2', repos = c('https://abdel-elsayed87.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/abdel-elsayed87/grin2/issues

Datasets:

On CRAN:

Conda:

3.00 score 1 stars 2 scripts 181 downloads 30 exports 37 dependencies

Last updated from:7c5c4bd9fd. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING233
source / vignettesOK272
linux-release-x86_64WARNING245
macos-release-arm64WARNING230
macos-oldrel-arm64WARNING205
windows-develWARNING178
windows-releaseWARNING227
windows-oldrelWARNING158
wasm-releaseOK168

Exports:alex.boxplotsalex.pathwayalex.prep.lsn.expralex.waterfall.plotalex.waterfall.prepcompute.gw.coordinatescount.hitsdefault.grin.colorsfind.gene.lsn.overlapsgenomewide.log10q.plotgenomewide.lsn.plotget.chrom.lengthget.ensembl.annotationgrin.assoc.lsn.outcomegrin.barpltgrin.lsn.boundariesgrin.oncoprint.mtxgrin.statsgrin.stats.lsn.plotKW.hit.expresslsn.transcripts.plotonco.print.propsorder.index.gene.dataorder.index.lsn.dataprep.binary.lsn.mtxprep.gene.lsn.dataprep.lsn.type.matrixprob.hitstop.alex.waterfall.plotswrite.grin.xlsx

Dependencies:circlizeclicolorspacecpp11data.tabledplyrfarverforcatsgenericsggplot2GlobalOptionsgluegtableisobandlabelinglatticelifecyclemagrittrMatrixpillarpkgconfigR6RColorBrewerrlangS7scalesshapestringistringrsurvivaltibbletidyselectutf8vctrsviridisLitewithrwritexl

Introduction to the GRIN2 Package

Abdelrahman Elsayed, PhD and Stanley Pounds, PhD

Rendered fromGRIN2.Rmdusingknitr::rmarkdownon May 19 2026.

Last update: 2025-06-23
Started: 2024-10-29

Readme and manuals

Help Manual

Help pageTopics
Generate Box Plots of Gene Expression by Lesion Groupsalex.boxplots
Visualize Lesion and Expression Data by Pathwayalex.pathway
Prepare Lesion and Expression Data for Kruskal Wallis Testalex.prep.lsn.expr
Generate Waterfall Plot of Lesion and Expression Dataalex.waterfall.plot
Prepare Lesion and Expression Data for Waterfall Plotsalex.waterfall.prep
Example Clinical Dataset for T-cell Acute Lymphoblastic Leukemia (T-ALL)clin_data
Compute Genome-wide Plotting Coordinatescompute.gw.coordinates
Count Gene Lesion Hitscount.hits
Assign Default GRIN Colorsdefault.grin.colors
Example T-ALL Gene Expression Datasetexpr_data
Find Gene Lesion Overlapsfind.gene.lsn.overlaps
Genome-wide -log10(q-value) Plotgenomewide.log10q.plot
Genome-wide Lesion Plotgenomewide.lsn.plot
Get Chromosome Lengthget.chrom.length
Get Ensembl Gene and Regulatory Features Annotation Dataget.ensembl.annotation
Associate Lesions with Clinical Outcomesgrin.assoc.lsn.outcome
GRIN Lesion Stacked Bar Plotgrin.barplt
GRIN Evaluation of Lesion Boundariesgrin.lsn.boundaries
GRIN OncoPrint-Compatible Lesion Matrixgrin.oncoprint.mtx
Execute GRIN Statistical Frameworkgrin.stats
GRIN Statistics Lesions Plotgrin.stats.lsn.plot
Chromosome Length Data (hg38)hg38_chrom_size
GRCh38 Chromosome Cytobandshg38_cytoband
Example Gene Annotation Data Filehg38_gene_annotation
Associate Lesion Groups with Gene ExpressionKW.hit.express
Example T-ALL Lesion Datasetlesion_data
Plot of Gene Lesions and Transcriptslsn.transcripts.plot
Oncoprint Proportions by Lesion Typeonco.print.props
Order and Index Gene Annotation Dataorder.index.gene.data
Order and Index Lesion Dataorder.index.lsn.data
Genes Annotated to Biological Pathwayspathways
Prepare Binary Lesion Matrixprep.binary.lsn.mtx
Prepare Gene and Lesion Data for GRIN Analysisprep.gene.lsn.data
Prepare Lesion Type Matrixprep.lsn.type.matrix
Find Probability of Locus Hitprob.hits
Generate Waterfall Plots for Top Significant Genestop.alex.waterfall.plots
Write GRIN Results to Excel Filewrite.grin.xlsx