Package: GRIN2 1.0

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_1.0.tar.gz
GRIN2_1.0.zip(r-4.5)GRIN2_1.0.zip(r-4.4)GRIN2_1.0.zip(r-4.3)
GRIN2_1.0.tgz(r-4.4-any)
GRIN2_1.0.tar.gz(r-4.5-noble)GRIN2_1.0.tar.gz(r-4.4-noble)
GRIN2_1.0.tgz(r-4.4-emscripten)GRIN2_1.0.tgz(r-4.3-emscripten)
GRIN2.pdf |GRIN2.html✨
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:

clin.data - Example T-ALL Dataset Clinical Data
expr.data - Example T-ALL Dataset Gene Expression Data
hg19.chrom.size - Chromosome Length Data File
hg19.gene.annotation - Example Gene Annotation Data File
hg19_cytoband - GRCh37 Chromosome Cytobands
hg38_cytoband - GRCh38 Chromosome Cytobands
lesion.data - Example T-ALL Dataset Lesion Data
pathways - List of Genes Annotated to a Group of Pathways

On CRAN:

3.30 score 30 exports 161 dependencies

Last updated 16 hours agofrom:ce7ea96b1c. Checks:OK: 1 WARNING: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 20 2024
R-4.5-win	WARNING	Nov 20 2024
R-4.5-linux	WARNING	Nov 20 2024
R-4.4-win	WARNING	Nov 20 2024
R-4.4-mac	WARNING	Nov 20 2024
R-4.3-win	WARNING	Nov 20 2024

Exports:alex.boxplots alex.pathway alex.prep.lsn.expr alex.waterfall.plot alex.waterfall.prep compute.gw.coordinates count.hits default.grin.colors find.gene.lsn.overlaps genomewide.log10q.plot genomewide.lsn.plot get.chrom.length get.ensembl.annotation grin.assoc.lsn.outcome grin.barplt grin.lsn.boundaries grin.oncoprint.mtx grin.stats grin.stats.lsn.plot KW.hit.express lsn.transcripts.plot onco.print.props order.index.gene.data order.index.lsn.data prep.binary.lsn.mtx prep.gene.lsn.data prep.lsn.type.matrix prob.hits top.alex.waterfall.plots write.grin.xlsx

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest doParallel dplyr EnsDb.Hsapiens.v75 ensembldb evaluate fansi farver fastmap filelock fontawesome forcats foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggplot2 GlobalOptions glue gridExtra gridGraphics gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 interp IRanges isoband iterators jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales shape snow SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr writexl xfun XML xml2 XVector yaml zlibbioc

Introduction to the GRIN2 Package

Abdelrahman Elsayed, PhD and Stanley Pounds, PhD

Rendered fromGRIN2.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-11-20
Started: 2024-10-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Prepare Box Plots of Expression Data by Lesion Groups	alex.boxplots
Associate Lesions with Expression Data on the Pathway Level	alex.pathway
Prepare Lesion and Expression Data for Kruskal-Wallis Test	alex.prep.lsn.expr
Prepare Waterfall Plot of Lesion and Expression Data	alex.waterfall.plot
Prepare Lesion and Expression Data for Waterfall Plots	alex.waterfall.prep
Example T-ALL Dataset Clinical Data	clin.data
Compute Genome-wide Coordinates	compute.gw.coordinates
Count Gene Lesion Hits	count.hits
Default GRIN Colors	default.grin.colors
Example T-ALL Dataset Gene Expression Data	expr.data
Find Gene Lesion Overlaps	find.gene.lsn.overlaps
Genomewide log10q Plot	genomewide.log10q.plot
Genome-wide Lesion Plot	genomewide.lsn.plot
Get Chromosome Length	get.chrom.length
Get Ensembl Gene and Regulatory Features Annotation Data	get.ensembl.annotation
Associate Lesions with Clinical Outcomes	grin.assoc.lsn.outcome
GRIN Bar Plot	grin.barplt
GRIN Evaluate Lesion Boundaries	grin.lsn.boundaries
GRIN OncoPrint Matrix	grin.oncoprint.mtx
GRIN Statistics Output	grin.stats
GRIN Statistics Lesions Plot	grin.stats.lsn.plot
GRCh37 Chromosome Cytobands	hg19_cytoband
Chromosome Length Data File	hg19.chrom.size
Example Gene Annotation Data File	hg19.gene.annotation
GRCh38 Chromosome Cytobands	hg38_cytoband
Associate Lesion with Expression Data Using Kruskal-Wallis Test	KW.hit.express
Example T-ALL Dataset Lesion Data	lesion.data
Lesions Gene Transcripts Plot	lsn.transcripts.plot
Oncoprint proportions	onco.print.props
Order Index Gene Data	order.index.gene.data
Order Index Lesion Data	order.index.lsn.data
List of Genes Annotated to a Group of Pathways	pathways
Prepare Binary Lesion Matrix	prep.binary.lsn.mtx
Prepare Gene and Lesion Data	prep.gene.lsn.data
Prepare Lesion Type Matrix	prep.lsn.type.matrix
Find Probablity of Locus Hit	prob.hits
Waterfall Plots for Lesion and Expression Data of Top Significant Genes	top.alex.waterfall.plots
Write GRIN Results	write.grin.xlsx