Package: hiReadsProcessor 1.43.0

Nirav V Malani

hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.

Authors:Nirav V Malani <[email protected]>

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hiReadsProcessor.pdf |hiReadsProcessor.html✨
hiReadsProcessor/json (API)
NEWS

# Install 'hiReadsProcessor' in R:

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

Datasets:

psl - PSL file output
seqProps - Sample Integration Sites Sequencing Data

On BioConductor:hiReadsProcessor-1.43.0(bioc 3.21)hiReadsProcessor-1.42.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencing preprocessing

4.18 score 7 scripts 222 downloads 48 exports 89 dependencies

Last updated 2 months agofrom:b964203895. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:addFeature addListNameToReads annotateSites blatListedSet blatSeqs chunkize clusterSites crossOverCheck decodeByBarcode dereplicateReads doRCtest extractFeature extractSeqs findAndRemoveVector findAndTrimSeq findBarcodes findIntegrations findLinkers findLTRs findPrimers findVector getIntegrationSites getSectorsForSamples getSonicAbund isuSites otuSites pairUpAlignments pairwiseAlignSeqs primerIDAlignSeqs pslCols pslToRangedObject read.BAMasPSL read.blast8 read.psl read.sampleInfo read.SeqFolder read.seqsFromSector removeReadsWithNs replicateReads sampleSummary splitByBarcode splitSeqsToFiles startgfServer trimSeqs troubleshootLinkers vpairwiseAlignSeqs write.listedDNAStringSet write.psl

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome cellranger cli codetools colorspace cpp11 crayon curl DelayedArray dplyr fansi farver foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue gtable hiAnnotator hms httr IRanges isoband iterators jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig prettyunits progress pwalign R6 RColorBrewer RCurl readxl rematch restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors scales snow sonicLength SparseArray SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml zlibbioc

Using hiReadsProcessor

Rendered fromTutorial.Rmdusingknitr::knitron Nov 29 2024.

Last update: 2017-09-12
Started: 2014-07-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add a specific feature/attribute to the sampleInfo object.	addFeature
Prepend name attribute of a list to DNAStringSet	addListNameToReads
Find the 5' primers and add results to SampleInfo object.	annotateSites
Align a listed DNAStringSet to a reference using gfClient or standalone BLAT.	blatListedSet
Align sequences using BLAT.	blatSeqs
Breaks an object into chunks of N size.	chunkize
Cluster/Correct values within a window based on their frequency given discrete factors	clusterSites
Remove values/positions which are overlapping between discrete groups based on their frequency.	crossOverCheck
Removes duplicate sequences from DNAStringSet object.	dereplicateReads
Test if pattern aligns better in +/- orientation.	doRCtest
Extract a specific feature/attribute of the sampleInfo object.	extractFeature
Extract sequences for a feature in the sampleInfo object.	extractSeqs
Find and trim vector sequence from reads.	findAndRemoveVector
Find and trim a short pattern sequence from the subject.	findAndTrimSeq
Demultiplex reads by their barcodes	decodeByBarcode findBarcodes
Find the integration sites and add results to SampleInfo object.	findIntegrations
Find the 3' linkers and add results to SampleInfo object.	findLinkers
Find the 5' LTRs and add results to SampleInfo object.	findLTRs
Find the 5' primers and add results to SampleInfo object.	findPrimers
Find vector DNA in reads and add results to SampleInfo object.	findVector
Obtain integration sites from BLAT output	getIntegrationSites
Get sectors for samples defined in the sampleInfo object.	getSectorsForSamples
Calculate breakpoint/sonic abundance of integration sites in a population	getSonicAbund
Functions to process LM-PCR reads from 454/Illumina data	hiReadsProcessor-package hiReadsProcessor
Bin values or make ISUs by assigning a unique ID to them within discrete factors.	isuSites
Bin values or make OTUs by assigning a unique ID to them within discrete factors.	otuSites
Pair up alignments in a GRanges object	pairUpAlignments
Align a short pattern to variable length target sequences.	pairwiseAlignSeqs
Align a short pattern with PrimerID to variable length target sequences.	primerIDAlignSeqs
PSL file output	psl
Return PSL file columns with classes	pslCols
Convert psl dataframe to GRanges	pslToRangedObject
Reads a BAM/SAM file and converts it into a PSL like format.	read.BAMasPSL
Read blast8 file(s) outputted by BLAT	read.blast8
Read PSL file(s) outputted by BLAT	read.psl
Read a sample information file and format appropriate metadata.	read.sampleInfo
Read contents of a sequencing folder and make a SimpleList object	read.SeqFolder
Read fasta/fastq given the path or sampleInfo object.	read.seqsFromSector
Remove sequences with ambiguous nucleotides.	removeReadsWithNs
Replicate sequences from DNAStringSet object using counts identifier or vector	replicateReads
Simple summary of a sampleInfo object.	sampleSummary
Sample Integration Sites Sequencing Data	seqProps
Split DNAStringSet object using first X number of bases defined by a vector.	splitByBarcode
Split DNA sequences into smaller files.	splitSeqsToFiles
Start/Stop a gfServer instance	startgfServer stopgfServer
Trim sequences from a specific side.	trimSeqs
Compare LTRed/Primed sequences to all linkers.	troubleshootLinkers
Align a short pattern to variable length target sequences.	vpairwiseAlignSeqs
Write a fasta file per sample in parallel	write.listedDNAStringSet
Write PSL file from dataframe or GRanges	write.psl