Reference

All functions

CIRCexplorer2()

Running CIRCexplorer2 parse command for circRNAs prediction from STAR or BWA alignment output

annoByGtfchipseq()

Annotating RSEM gene.results using ENSEMBL gtf and refGenome CRAN package

anovaLike()

A function allowing the identification of differentially expressed genes if multiple groups are provided.

bowtie2()

Running bowtie2

bowtie2Index()

Generating bowtie2 genome index

bwa()

Running bwa, Li and Durbin Bioinformatics, 2009 Jul 15;25(14):1754-60

bwaIndex()

Generating bwa genome index

bwaIndexUcsc()

Generating bwa genome index for GATK variant call

cdhit()

A function to execute CD-HIT

chipseq()

Detection and annotation of TF binding sites and histone marks, based on the workflow used in Galli et al Mol Cell. 2015 Oct 15;60(2):328-37

chipseqCounts()

Running MACS & SICER workflow NOT READY FOR STABLE check it!

circrnaAnnotations()

Annotation of a list of circRNAs

circrnaBSJunctions()

Running CircHunter circRNA backsplicing sequence reconstruction module

circrnaClassification()

Running CircHunter circRNA classification module

circrnaMergePredictions()

Function to merge different circRNA lists predicted from one of the supported circRNA prediction tools.

circrnaOverlapResults()

Running circRNA prediction overlap

circrnaPrepareFiles()

Function to prepare the CircHunter reference annotations

circrnaQuantification()

Running CircHunter circRNA quantification module

circrnaReformat()

Running circRNA reformat script

ciri2()

Running CIRI v2 tool for circRNAs prediction

ciriAS()

Running CIRI_AS tool for circRNAs structure prediction

cutadapt()

Function to execute Cutadapt on RNA-Seq reads

deeptoolBwig()

Create a bigWig from the output of bowtie2

demultiplexing()

Generating running bcl2fastq

dockerTest()

Testing if Docker is installed

downloadContainers()

Download for the first time all containers embedded in the workflows

experimentPower()

A wrapper function for experiment_power from RnaSeqSampleSize Bioconductor package

fastq2fasta()

A function to handle the conversion from fastq to fasta

fastqc()

A function to handle a docker containier executing fastqc

filterCounts()

Filter a count table using a table of DE from wrapperDeseq2

gatkDNA()

Running realignment and recalibration, GATK

getInfo()

Downloading the full set of genes information from HGNC

hashclone()

HashClone running A function to handle a hashclone docker container NOT READY for STABLE RELEASE, YET

heatmapBase()

hfc, heatmap for clustering

heatmaply()

Function to produce an interactive heatmap using plot.ly

kraken()

A function executing kraken

macs2()

A function to handle a MACS2 containier

mergeData()

Function to merge different circRNA lists from CIRI 2

mirnaCounts()

Counting miRNAs, Cordero et al. PLoS One. 2012;7:e31630

mirnaCovar()

Adding covariates and batch information to miRNAseq raw counts output

multiQC()

A function to handle a docker containier executing MultiQC

oncosnp()

A function to handle a docker containier executing CNV calculation. Only supporting hg19

oncosnpAnnotation()

A function to associate CNV generated by oncSNP starting from log R ratio and B allel frequences, generated by SNP arrays, to gene symbols

pca()

generating a PCA from counts, FPKM and TPM tables from rnaseqCounts outuputs

platypus()

Platypus analysis NOT READY TO GO ON STABLE missing test set

platypusFilter()

Platypus filter analysis NOT READY TO GO ON STABLE to be used in case the full platypus workflow fail.

prepare4expands()

A function to handle a docker containier preparing the file needed for expanse

pubmedNet()

Creating networks on the basis of the links between genes ids and pubmedid

rnaseqCounts()

Running RNAseq counting workflow for a single sample

rsemBw()

Creating a bigwig using RSEM

rsemanno()

Annotating RSEM gene.results using ENSEMBL annotation

rsemannoByGtf()

Annotating RSEM gene.results using ENSEMBL gtf and refGenome CRAN package

rsemstar()

Running RSEM, Li and Dewey BMC Bioinformatics 2011 12:323

rsemstarIndex()

Generating rsem-star genome index

rsemstarUscsIndex()

Generating rsem-star genome index

runDocker()

Run docker container

salmonAnnotation()

A function to annotate salmon output

salmonCounts()

A function to handle a salmon docker container

salmonIndex()

A function to create a Salmon pseudo reference

sample2experiment()

generating counts, FPKM and TPM tables from rnaseqCounts outuputs

sampleSize()

A wrapper function for sample_size_distribution function from RnaSeqSampleSize Bioconductor package

skeleton()

A skeleton function to handle a docker containier

skewer()

Running skewer, an adapter trimmer application, Jiang et al BMC Bioinformatics201415:182

skewerXSergio()

Running skewer, an adapter trimmer application, Jiang et al BMC Bioinformatics201415:182

sncRNA()

Running small RNA-seq single-end reads alignment and quantification using BWA and custom scripts

snvPreprocessing()

Running indel relignment and quality recalibration on bam generated by bwa function NOT READY TO GO ON STABLE

sraDownload()

A function to handle fasterq-dumper SRA to download SRA fastq files

star()

Running Star two steps for variant calls

star2steps()

Running Star two steps for variant calls

starChimeric()

Running Star to detect chimeric transcripts on paired-end sequences

starChipIndex()

Preparing the bed file required by starchip to detect circular RNAs on paired-end sequences

starchipCircle()

Running starchip to detect circular RNAs on paired-end sequences

testSeqbox()

Testing the SeqBox basic installation

trimFasta()

A function to execute seqtk trimming

wrapperCiri()

Wrapper function for circRNAs prediction using CIRI 2

wrapperDeseq2()

A wrapper function for deseq2 for two groups only

wrapperPdx()

Running PDX data preprocessing TO BE REVISED

wrapperSTARChip()

Wrapper function for circRNAs prediction using STARChip

wrapperSalmon()

A function to estimate counts using Salmon quasi-alignment

xenome()

Running xenome, https://github.com/data61/gossamer/

xenomeIndex()

Generating xenome genome indexes