Man pages for kendomaniac/docker4seq
Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

anovaLikeA function allowing the identification of differentially...
bwaRunning bwa, Li and Durbin Bioinformatics, 2009 Jul...
bwaIndexGenerating bwa genome index
bwaIndexUcscGenerating bwa genome index for GATK variant call
chipseqDetection and annotation of TF binding sites and histone...
chipseqCountsRunning MACS & SICER workflow NOT READY FOR STABLE check it!
demultiplexingGenerating running bcl2fastq
dockerTestTesting if Docker is installed
downloadContainersDownload for the first time all containers embedded in the...
experimentPowerA wrapper function for experiment_power from RnaSeqSampleSize...
fastqcA function to handle a docker containier executing fastqc
filterCountsFilter a count table using a table of DE from wrapperDeseq2
gatkDNARunning realignment and recalibration, GATK
hashcloneHashClone running A function to handle a hashclone docker...
heatmapBasehfc, heatmap for clustering
mirnaCountsCounting miRNAs, Cordero et al. PLoS One. 2012;7:e31630
mirnaCovarAdding covariates and batch information to miRNAseq raw...
multiQCA function to handle a docker containier executing MultiQC
oncosnpAnnotationA function to associate CNV generated by oncSNP starting from...
pcagenerating a PCA from counts, FPKM and TPM tables from...
platypusPlatypus analysis NOT READY TO GO ON STABLE missing test set
platypusFilterPlatypus filter analysis NOT READY TO GO ON STABLE to be used...
rnaseqCountsRunning RNAseq counting workflow for a single sample
rsemannoAnnotating RSEM gene.results using ENSEMBL annotation
rsemannoByGtfAnnotating RSEM gene.results using ENSEMBL gtf and refGenome...
rsemBwCreating a bigwig using RSEM
rsemstarRunning RSEM, Li and Dewey BMC Bioinformatics 2011 12:323
rsemstarIndexGenerating rsem-star genome index
rsemstarUscsIndexGenerating rsem-star genome index
runDockerRun docker container
salmonAnnotationA function to annotate salmon output
salmonCountsA function to handle a salmon docker container
salmonIndexA function to create a Salmon pseudo reference
sample2experimentgenerating counts, FPKM and TPM tables from rnaseqCounts...
sampleSizeA wrapper function for sample_size_distribution function from...
skeletonA skeleton function to handle a docker containier
skewerRunning skewer, an adapter trimmer application, Jiang et al...
sncRNARunning small RNA-seq single-end reads alignment and...
star2stepsRunning Star two steps for variant calls
starChimericRunning Star to detect chimeric transcripts on paired-end...
starchipCircleRunning starchip to detect circular RNAs on paired-end...
starChipIndexPreparing the bed file required by starchip to detect...
testSeqboxTesting the SeqBox basic installation
wrapperDeseq2A wrapper function for deseq2 for two groups only
wrapperPdxRunning PDX data preprocessing TO BE REVISED
wrapperSalmonA function to estimate counts using Salmon quasi-alignment
xenomeRunning xenome, https://github.com/data61/gossamer/
xenomeIndexGenerating xenome genome indexes
kendomaniac/docker4seq documentation built on Aug. 26, 2018, 2:13 p.m.