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.

sequencingpreprocessing

4.18 score 7 scripts 258 downloads 48 exports 88 dependencies

Last updated 4 months agofrom:b964203895. Checks:1 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
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R-4.5-linuxNOTEJan 28 2025
R-4.4-winNOTEJan 28 2025
R-4.4-macNOTEJan 28 2025
R-4.3-winNOTEJan 28 2025
R-4.3-macNOTEJan 28 2025

Exports:addFeatureaddListNameToReadsannotateSitesblatListedSetblatSeqschunkizeclusterSitescrossOverCheckdecodeByBarcodedereplicateReadsdoRCtestextractFeatureextractSeqsfindAndRemoveVectorfindAndTrimSeqfindBarcodesfindIntegrationsfindLinkersfindLTRsfindPrimersfindVectorgetIntegrationSitesgetSectorsForSamplesgetSonicAbundisuSitesotuSitespairUpAlignmentspairwiseAlignSeqsprimerIDAlignSeqspslColspslToRangedObjectread.BAMasPSLread.blast8read.pslread.sampleInforead.SeqFolderread.seqsFromSectorremoveReadsWithNsreplicateReadssampleSummarysplitByBarcodesplitSeqsToFilesstartgfServertrimSeqstroubleshootLinkersvpairwiseAlignSeqswrite.listedDNAStringSetwrite.psl

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomecellrangerclicodetoolscolorspacecpp11crayoncurlDelayedArraydplyrfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehiAnnotatorhmshttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigprettyunitsprogresspwalignR6RColorBrewerRCurlreadxlrematchrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowsonicLengthSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

Using hiReadsProcessor

Rendered fromTutorial.Rmdusingknitr::knitron Jan 28 2025.

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

Readme and manuals

Help Manual

Help pageTopics
Add a specific feature/attribute to the sampleInfo object.addFeature
Prepend name attribute of a list to DNAStringSetaddListNameToReads
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 factorsclusterSites
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 barcodesdecodeByBarcode 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 outputgetIntegrationSites
Get sectors for samples defined in the sampleInfo object.getSectorsForSamples
Calculate breakpoint/sonic abundance of integration sites in a populationgetSonicAbund
Functions to process LM-PCR reads from 454/Illumina datahiReadsProcessor-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 objectpairUpAlignments
Align a short pattern to variable length target sequences.pairwiseAlignSeqs
Align a short pattern with PrimerID to variable length target sequences.primerIDAlignSeqs
PSL file outputpsl
Return PSL file columns with classespslCols
Convert psl dataframe to GRangespslToRangedObject
Reads a BAM/SAM file and converts it into a PSL like format.read.BAMasPSL
Read blast8 file(s) outputted by BLATread.blast8
Read PSL file(s) outputted by BLATread.psl
Read a sample information file and format appropriate metadata.read.sampleInfo
Read contents of a sequencing folder and make a SimpleList objectread.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 vectorreplicateReads
Simple summary of a sampleInfo object.sampleSummary
Sample Integration Sites Sequencing DataseqProps
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 instancestartgfServer 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 parallelwrite.listedDNAStringSet
Write PSL file from dataframe or GRangeswrite.psl