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RNASeqGenie (version 1.0.44)

Runs the RNA-Seq Pipeline

Description

Functions to run the RNA-Seq pipeline and help set up a run

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Version

Version

1.0.44

License

Artistic-2.0

Maintainer

Last Published

February 15th, 2017

Functions in RNASeqGenie (1.0.44)

buildCountsGRangesLists

Build GRanges for Counts and RPKM
getUnpairedMult

Extract Parts of Paired-End Alignment Data That Map Qniquely
getwgR_GRanges

getwgR_GRanges
detectRRNA454

Detect rRNA Contamination in 454 Reads
makeConfigFile

Create GNE RNA-Seq pipeline config file
dedupeAndRevcompFasta

dedupeAndRevcompFasta
readRNASeqEnds

Read Paired End Bam Files
getRandomAlignCutoff

getRandomAlignCutoff
tableExonsHit

Get exon groups hit tally from a GRangesList
readGsnapRNASeqOutputEnds

Read Gsnap Paired-End Output
.test

.test
detectRRNA

Detect rRNA Contamination in Reads
getExonGroupID

getExonGroupID
extractJunctions

extractJunctions
exonGroupingsFromMatchMatrix

Get hits by exon group
sampleFromPairedEnd

sampleFromPairedEnd
runPipeline

Run the RNA-Seq Pipeline
getDEXSeqDataFrame

Get DEXSeq data.frame
mergeLanes

Merge *Genie Pipeline Output Data
fixBamMDString

Fix malformed MD strings in BAM files
getMitochondrialGeneGRanges

getMitochondrialGeneGRanges
mergeBAMsAcrossDirs

mergeBAMsAcrossDirs
processRawFastq

processRawFastq
recordObjectMemorySizes

recordObjectMemorySizes
.appendExonHitsGRanges

.appendExonHitsGRanges
buildAlignerParams

Build Aligner Command-Line Args
getHinvGRanges

getHinvGRanges
getHinvCodingGRanges

getHinvCodingGRanges
reportPipelineQA

Generate RNA-Seq Pipeline QA Report
rpkm_old

rpkm_old
detectNcRNA

Detect ncRNA Read Hits
rpkm

Calculates RPKMs
processGsnapResults

Process Gsnap RNA-Seq BAM output
getFusionGRangesList

Get GRangesList of fusion ends from a BAM file
.help.ESS

.help.ESS
createSummaryTable

createSummaryTable
detectAdapterContam

Detect Adapter Contamination in Reads
getmm9ncRNAGRanges

getmm9ncRNAGRanges
countGenomicFeatures

Count RNA-Seq Pipeline Genomic Features
consolidateByRead

Consolidate Paired-End Alignments by Read Names
mvBAMFixedFiles

mvBAMFixedFiles
fastqToBAM

fastqToBAM
installRRNAGmapIIT

Install rRNA Gmap IIT
trimReads

trimReads
verifyFixedBAMsAreValid

Verify BAMs with Fixed MD Strings are Valid
appendOverlappingExons

Append overlapping exons
verifyPipelineGsnapOutput

Verify gsnap output