R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 129 found.
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FastQStreamer.getReads (Package: HTSeqGenie) : Get FastQ reads from the FastQ streamer

Get FastQ reads from the FastQ streamer

● Data Source: BioConductor
● Keywords: internal
● Alias: FastQStreamer.getReads
● 0 images

FastQStreamer.init (Package: HTSeqGenie) : Open a streaming connection to a FastQ file

Open a streaming connection to a FastQ file

● Data Source: BioConductor
● Keywords: internal
● Alias: FastQStreamer.init
● 0 images

FastQStreamer.release (Package: HTSeqGenie) : Close the FastQStreamer

Close the FastQStreamer

● Data Source: BioConductor
● Keywords: internal
● Alias: FastQStreamer.release
● 0 images

HTSeqGenie (Package: HTSeqGenie) : Package overview

The HTSeqGenie package is a robust and efficient software to analyze high-throughput sequencing experiments in a reproducible manner. It supports the RNA-Seq and Exome-Seq protocols and provides: quality control reporting (using the ShortRead package), detection of adapter contamination, read alignment versus a reference genome (using the gmapR package), counting reads in genomic regions (using the GenomicRanges package), and read-depth coverage computation.

● Data Source: BioConductor
● Keywords: package
● Alias: HTSeqGenie
● 0 images

TP53GenomicFeatures (Package: HTSeqGenie) : Demo genomic features around the TP53 gene

Build the genomic features of the TP53 demo region

● Data Source: BioConductor
● Keywords:
● Alias: TP53GenomicFeatures
● 0 images

alignReads (Package: HTSeqGenie) : Align reads against genome

Align reads against genome

● Data Source: BioConductor
● Keywords: internal
● Alias: alignReads
● 0 images

alignReadsChunk (Package: HTSeqGenie) : Genomic alignment

Genomic alignment using gsnap.

● Data Source: BioConductor
● Keywords: internal
● Alias: alignReadsChunk
● 0 images

analyzeVariants (Package: HTSeqGenie) : Calculate and process Variants

Calculate and process Variants

● Data Source: BioConductor
● Keywords:
● Alias: analyzeVariants
● 0 images

bamCountUniqueReads (Package: HTSeqGenie) : Uniquely count number of reads in bam file

Uniquely count number of reads in bam file

● Data Source: BioConductor
● Keywords: internal
● Alias: bamCountUniqueReads
● 0 images

buildConfig (Package: HTSeqGenie) : Build a configuration file based on a list of parameters

Build a configuration file based on a list of parameters

● Data Source: BioConductor
● Keywords: internal
● Alias: buildConfig
● 0 images