Package: SingleMoleculeGenomicsIO 0.1.9

Michael Stadler

SingleMoleculeGenomicsIO: Tools for reading single molecule genomics data

Provides tools for reading of single-molecule genomics data from different file formats in R. The package includes functions for reading collapsed or read-level data from modBAM, bedMethyl and `modkit extract` tabular files, as well as C-to-T conversion based BAM files, as `SummarizedExperiment` objects.

Authors:Michael Stadler [aut, cre], Charlotte Soneson [aut], Panagiotis Papasaikas [aut], Sebastien Smallwood [aut], Friedrich Miescher Institute for Biomedical Research [cph]

# Install 'SingleMoleculeGenomicsIO' in R:

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

Bug tracker:https://github.com/fmicompbio/singlemoleculegenomicsio/issues

Pkgdown/docs site:https://fmicompbio.github.io

Uses libs:

curl– Easy-to-use client-side URL transfer library
bzip2– High-quality block-sorting file compressor library
xz-utils– XZ-format compression library
zlib– Compression library
c++– GNU Standard C++ Library v3

On CRAN:

epigenetics longread curl bzip2 xz-utils zlib cpp

4.06 score 12 scripts 33 exports 78 dependencies

Last updated from:8c2db76b51. Checks:13 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	NOTE	431
linux-devel-x86_64	NOTE	480
source / vignettes	OK	550
linux-release-arm64	NOTE	431
linux-release-x86_64	NOTE	494
macos-release-arm64	NOTE	620
macos-release-x86_64	NOTE	892
macos-oldrel-arm64	NOTE	476
macos-oldrel-x86_64	NOTE	735
windows-devel-arm64	NOTE	749
windows-devel-x86_64	NOTE	609
windows-release-arm64	NOTE	744
windows-release-x86_64	NOTE	489
windows-oldrel-x86_64	NOTE	550
wasm-release	OK	204

Exports:addReadLevelAssay addReadStats addSeqContext annotateReadSegments calcReadStats checkSEValidity countAlignmentsInBam countMismatchStatePairs countStatePairs estimateNoise estimateSNR expandSEToBaseSpace extractColDataColumns extractSeqContext filterPositions filterReads filterReadsModBam flattenReadLevelAssay getBaseCoverageForBam getReadLevelAssayNames getReadLevelColDataNames getReadNamesBySample plotReadStats readBedMethyl readMismatchBam readModBam readModkitExtract refargToDNAStringSet regionStringToGRanges regroupReads regroupReadsByColData sampleEntropy subsetReads

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome cigarillo cli codetools cpp11 crayon curl data.table DelayedArray dplyr farver formatR futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig purrr R6 RColorBrewer Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs viridisLite withr XML XVector yaml

SingleMoleculeGenomicsIO

Rendered fromSingleMoleculeGenomicsIO.Rmdusingknitr::rmarkdown

Last update: 2026-05-08
Started: 2025-12-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add a read-level assay to a SummarizedExperiment object	addReadLevelAssay
Add sequence context around positions of interest to a SummarizedExperiment	addSeqContext
Add read segment annotation	annotateReadSegments
Calculate or add summary statistics for read-level base modification data	addReadStats calcReadStats
Check internal consistency of SummarizedExperiment object	checkSEValidity
Count alignments in an indexed bam file	countAlignmentsInBam
Count pairs of modified bases by distance and modification state for bam files where modifications are indicated by sequence mismatches	countMismatchStatePairs
Count pairs of modified bases by distance and modification state	countStatePairs
Estimation of noise variance for time series.	estimateNoise
Estimate a time series Signal to Noise Ratio (SNR) given total and noise variance components and (optionally) a background noise model.	estimateSNR
Expand the rows of a 'RangedSummarizedExperiment' to single base resolution.	expandSEToBaseSpace
Extract one or more (possibly nested) columns from the colData of a SummarizedExperiment object	extractColDataColumns
Extract the sequence context around positions of interest	extractSeqContext
Filter positions	filterPositions
Filter reads	filterReads
Write bam records from 'infile' to 'outfile' if they pass filter criteria.	filterReadsModBam
Summarize a read-level object to sample-level	flattenReadLevelAssay
Get base coverage histogram for a BAM file	getBaseCoverageForBam
Get names of assays containing read-level data	getReadLevelAssayNames
Get names of colData columns containing read-level data	getReadLevelColDataNames
Get list of read names by sample from SummarizedExperiment object	getReadNamesBySample
Plot distribution of QC statistics	plotReadStats
Read collapsed single-molecule footprinting data from a 'bedMethyl' file	readBedMethyl
Read base modifications from "C-to-T" bam file(s)	readMismatchBam
Read base modifications from bam file(s)	readModBam
Read modkit extract file(s)	readModkitExtract
Convert a supported reference sequence argument to a DNAStringSet	refargToDNAStringSet
Convert character region(s) to a 'GRanges' object	regionStringToGRanges
Regroup reads	regroupReads regroupReadsByColData
Sample Entropy of Time series signal	sampleEntropy
Subset the reads from read-level assays	subsetReads