| annoByGtfchipseq | Annotating RSEM gene.results using ENSEMBL gtf and refGenome... |
| anovaLike | A function allowing the identification of differentially... |
| bowtie2 | Running bowtie2 |
| bowtie2Index | Generating bowtie2 genome index |
| bwa | Running bwa, Li and Durbin Bioinformatics, 2009 Jul... |
| 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... |
| chipseqCounts | Running MACS & SICER workflow NOT READY FOR STABLE check it! |
| CIRCexplorer2 | Running CIRCexplorer2 parse command for circRNAs prediction... |
| circrnaAnnotations | Annotation of a list of circRNAs |
| circrnaBSJunctions | Running CircHunter circRNA backsplicing sequence... |
| circrnaClassification | Running CircHunter circRNA classification module |
| circrnaMergePredictions | Function to merge different circRNA lists predicted from one... |
| 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... |
| experimentPower | A wrapper function for experiment_power from RnaSeqSampleSize... |
| 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... |
| 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... |
| multiQC | A function to handle a docker containier executing MultiQC |
| oncosnp | A function to handle a docker containier executing CNV... |
| oncosnpAnnotation | A function to associate CNV generated by oncSNP starting from... |
| pca | generating a PCA from counts, FPKM and TPM tables from... |
| 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... |
| prepare4expands | A function to handle a docker containier preparing the file... |
| pubmedNet | Creating networks on the basis of the links between genes ids... |
| rnaseqCounts | Running RNAseq counting workflow for a single sample |
| rsemanno | Annotating RSEM gene.results using ENSEMBL annotation |
| rsemannoByGtf | Annotating RSEM gene.results using ENSEMBL gtf and refGenome... |
| rsemBw | Creating a bigwig using RSEM |
| 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... |
| sampleSize | A wrapper function for sample_size_distribution function from... |
| skeleton | A skeleton function to handle a docker containier |
| skewer | Running skewer, an adapter trimmer application, Jiang et al... |
| skewerXSergio | Running skewer, an adapter trimmer application, Jiang et al... |
| sncRNA | Running small RNA-seq single-end reads alignment and... |
| snvPreprocessing | Running indel relignment and quality recalibration on bam... |
| sraDownload | A function to handle fasterq-dumper SRA to download SRA fastq... |
| 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... |
| starchipCircle | Running starchip to detect circular RNAs on paired-end... |
| starChipIndex | Preparing the bed file required by starchip to detect... |
| 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 |
| wrapperSalmon | A function to estimate counts using Salmon quasi-alignment |
| wrapperSTARChip | Wrapper function for circRNAs prediction using STARChip |
| xenome | Running xenome, https://github.com/data61/gossamer/ |
| xenomeIndex | Generating xenome genome indexes |
