Package: GenomeScaleEmbeddings 0.0.0.9000

GenomeScaleEmbeddings: Exploring Genome Scale Embeddings Parquet Files

Some explorations of the genomics embedding from the paper "Incorporating LLM Embeddings for Variation Across the Human Genome" <https://arxiv.org/html/2509.20702v1>

Authors:Sounkou Mahamane Toure [aut, cre]

GenomeScaleEmbeddings_0.0.0.9000.tar.gz
GenomeScaleEmbeddings_0.0.0.9000.zip(r-4.7)GenomeScaleEmbeddings_0.0.0.9000.zip(r-4.6)GenomeScaleEmbeddings_0.0.0.9000.zip(r-4.5)
GenomeScaleEmbeddings_0.0.0.9000.tgz(r-4.6-any)GenomeScaleEmbeddings_0.0.0.9000.tgz(r-4.5-any)
GenomeScaleEmbeddings_0.0.0.9000.tar.gz(r-4.7-any)GenomeScaleEmbeddings_0.0.0.9000.tar.gz(r-4.6-any)
GenomeScaleEmbeddings_0.0.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GenomeScaleEmbeddings/json (API)

# Install 'GenomeScaleEmbeddings' in R:

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

Bug tracker:https://github.com/sounkou-bioinfo/genomescaleembeddings/issues

On CRAN:

2.00 score 2 scripts 13 exports 51 dependencies

Last updated from:6a7f6dd578. Checks:7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	135
source / vignettes	OK	262
linux-release-x86_64	WARNING	131
macos-release-arm64	WARNING	84
macos-oldrel-arm64	WARNING	98
windows-devel	WARNING	84
windows-release	WARNING	78
windows-oldrel	WARNING	87
wasm-release	OK	187

Exports:attachHoubaBigMatrix CopyParquetToDuckDB correlatePCWithPosition DatasetParquetUrlList embeddingSummary getPcaScores houbaPCA infoSummary IterateEmbeddingsMatrixBatches OpenRemoteParquetView plotPcaDims plotPCSpatialCorrelation writeEmbeddingsHoubaFromDuckDB

Dependencies:askpass BH bigmemory bigmemory.sri bigPCAcpp cachem cli collections cpp11 curl DBI dplyr duckdb duckplyr evaluate farver fastmap generics ggplot2 glue gtable highr houba httr2 isoband jsonlite knitr labeling lifecycle magrittr memoise openssl pillar pkgconfig R6 rappdirs RColorBrewer Rcpp rlang S7 scales sys tibble tidyselect utf8 uuid vctrs viridisLite withr xfun yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Attach a houba file and return the bigmemory::big.matrix	attachHoubaBigMatrix
Copy remote parquet files into a local DuckDB database file using explicit URLs	CopyParquetToDuckDB
Compute correlation between PC scores and genomic position, per chromosome	correlatePCWithPosition
List of the huggingface datasets for the paper "Incorporating LLM Embeddings for Variation Across the Human Genome"	DatasetParquetUrlList
Quick summary for houba mmatrix	embeddingSummary
Get PCA scores from houbaPCA result	getPcaScores
PCA using bigPCAcpp on houba mmatrix or bigmemory::big.matrix	houbaPCA
Quick summary for houba info mmatrix	infoSummary
Iterate over embeddings as matrix batches from a local DuckDB file	IterateEmbeddingsMatrixBatches
Open remote parquet files as a DuckDB VIEW and return as tibble (minimal, http(s) only)	OpenRemoteParquetView
Plot PCA dimensions using ggplot2, colored by annotation	plotPcaDims
Plot spatial correlation between PC scores and genomic position, faceted by chromosome	plotPCSpatialCorrelation
Write embeddings to houba mmatrix and return info as data.frame from a local DuckDB file	writeEmbeddingsHoubaFromDuckDB