Package: selexprepR 0.99.6

Marco Rota Negroni

selexprepR: Preprocessing Public HT-SELEX Sequencing Data

Provides reproducible preprocessing for high-throughput SELEX sequencing data. Supports primer inference, extraction of random regions, sparse sequence counting across rounds, quality control, and provenance manifests. Public-study discovery and checksum-aware ENA FASTQ download planning are included for reproducible data acquisition.

Authors:Marco Rota Negroni [aut, cre]

selexprepR_0.99.6.tar.gz
selexprepR_0.99.6.zip(r-4.7-any)selexprepR_0.99.6.zip(r-4.6-any)selexprepR_0.99.6.zip(r-4.5-any)
selexprepR_0.99.6.tgz(r-4.6-any)selexprepR_0.99.6.tgz(r-4.5-any)
selexprepR_0.99.6.tar.gz(r-4.7-any)selexprepR_0.99.6.tar.gz(r-4.6-any)
selexprepR_0.99.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
selexprepR/json (API)

# Install 'selexprepR' in R:

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

Bug tracker:https://github.com/marcorotanegroni/selexprepr/issues

Datasets:

selexprep_public_catalog - Curated public HT-SELEX catalog

On CRAN:

software dataimport preprocessing qualitycontrol sequencing

3.18 score 3 scripts 21 exports 35 dependencies

Last updated from:c2f7abdc07. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	148
linux-devel	OK	252
source / vignettes	OK	198
linux-release	OK	213
macos-release	OK	173
macos-oldrel	OK	154
windows-devel	OK	161
windows-release	OK	183
windows-oldrel	OK	160
wasm-release	OK	100

Exports:build_selexprep_manifest fetch_selexprep_reads infer_selexprep_rounds inspect_selexprep_accession read_library_report read_selexprep_counts read_selexprep_fastq read_selexprep_inputs read_selexprep_manifest reverse_complement run_selexprep run_selexprep_files selexprep_catalog selexprep_count selexprep_demultiplex selexprep_detect selexprep_extract selexprep_qc write_library_report write_selexprep_counts write_selexprep_manifest

Dependencies:abind askpass Biobase BiocGenerics Biostrings cli crayon curl DelayedArray digest generics GenomicRanges glue httr2 IRanges jsonlite lattice lifecycle magrittr Matrix MatrixGenerics matrixStats openssl R6 rlang S4Arrays S4Vectors Seqinfo SparseArray SummarizedExperiment sys vctrs withr xml2 XVector

Preprocessing an HT-SELEX study

Rendered fromselexprep.Rmdusingknitr::rmarkdown

Last update: 2026-10-14
Started: 2026-07-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Build an R-native reproducibility manifest	build_selexprep_manifest
Fetch FASTQ files from an ENA inspection	fetch_selexprep_reads
Infer SELEX round assignments from public metadata	infer_selexprep_rounds
Inspect public sequencing metadata at ENA	inspect_selexprep_accession
Plot SELEX quality-control diagnostics	plot.selexprep_qc
Read a LibraryReport JSON file	read_library_report
Read a selexprep count table	read_selexprep_counts
Read sequences from a FASTQ file	read_selexprep_fastq
Read FASTQ files into round-aware pipeline inputs	read_selexprep_inputs
Read a selexprep manifest JSON file	read_selexprep_manifest
Reverse-complement nucleotide sequences	reverse_complement
Run the in-memory SELEX preprocessing workflow	run_selexprep
Run selexprepR directly from FASTQ files	run_selexprep_files
Query the bundled public HT-SELEX study catalog	selexprep_catalog
Count unique SELEX sequences	selexprep_count
Demultiplex SELEX reads with user-supplied barcodes	selexprep_demultiplex
Detect SELEX library structure and constant regions	selexprep_detect
Extract random regions from a SELEX library	selexprep_extract
Curated public HT-SELEX catalog	selexprep_public_catalog
Quality-control summary for a SELEX count experiment	selexprep_qc
selexprepR result objects	selexprep-classes selexprep_extraction selexprep_fetch_result selexprep_inspection selexprep_library_report selexprep_manifest selexprep_read_inputs
Write a LibraryReport as deterministic JSON	write_library_report
Write a selexprep count table	write_selexprep_counts
Write a selexprep manifest as deterministic JSON	write_selexprep_manifest