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A container for coding sequence annotation information.
● Data Source:
BioConductor
● Keywords: classes
● Alias: CDSSet, CDSSet-class
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Creates a SpliceRList object from two GRanges objects, an assembly id, and a source id. The first GRanges, transcript_features, containing a list of transcripts, and including the columns gene_id for gene id, tx_id for transcript id, sample_1 and sample_2 for sample identifiers, expression_1 and expression_2 for expression values for sample 1 and sample 2, respectively (typically FPKM values or some other normalized count values), and additional optional columns (see prepareCuff). The second, exon_features, containing a list of exons, and including the columns gene_id for gene id and tx_id for transcript id. Assembly id, denoting genome assembly ('hg19', 'hg18', 'mm9', etc.) Source id, denoting source of transcript assembly (currently 'cufflinks' or 'other') Note, that the cromosome identifiers should match the assembly. For experiments
● Data Source:
BioConductor
● Keywords: classes
● Alias: SpliceRList, SpliceRList-class
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annotatePTC
(Package: spliceR) :
PTC and NMD-sensitivity detection from assembled RNA-seq data
PTC and NMD-sensitivity detection from assembled RNA-seq data.
● Data Source:
BioConductor
● Keywords:
● Alias: annotatePTC
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conditions
(Package: spliceR) :
Returns sample condictions of an SpliceRList or an CuffSet object
Returns samples/condictions of an SpliceRList or an CuffSet object.
● Data Source:
BioConductor
● Keywords:
● Alias: conditions
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dim
(Package: spliceR) :
Retrieve the Dimensions of a SpliceRList
Retrieve the number of (transcripts) contained in SpliceRList.
● Data Source:
BioConductor
● Keywords:
● Alias: dim.SpliceRList, length.SpliceRList
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generateGTF
(Package: spliceR) :
Generate GTF files for transcript visualization in genome browsers
Generate GTF files for transcript visualization in genome browsers.
● Data Source:
BioConductor
● Keywords:
● Alias: generateGTF
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getCDS
(Package: spliceR) :
Retrieve CDS information from UCSC
Retrieve CDS information from a selected repository from UCSC genome browser repositories.
● Data Source:
BioConductor
● Keywords:
● Alias: getCDS
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preSpliceRFilter
(Package: spliceR) :
Filters on spliceR-lists for reduction of data sets
Applies a number of filters on a spliceR object to reduce data set size before running downstream analyses.
● Data Source:
BioConductor
● Keywords:
● Alias: preSpliceRFilter
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prepareCuff
(Package: spliceR) :
Prepare assembled RNA-seq data from Cufflinks for spliceR
Prepare assembled RNA-seq data from Cufflinks for spliceR.
● Data Source:
BioConductor
● Keywords:
● Alias: prepareCuff
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Prepare the Cufflinks example data set.
● Data Source:
BioConductor
● Keywords:
● Alias: prepareCuffExample
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providing 
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