Gene and Splice Site Annotation Using Annotation Data from 'Ensembl' and 'UCSC' Genome Browsers

Contains functionalities for importing and managing downloaded genome annotation data from 'Ensembl' genome browser (European Bioinformatics Institute, < https://www.ensembl.org>) and from 'UCSC' genome browser (University of California, Santa Cruz, < https://genome.ucsc.edu/>) and annotation routines for genomic positions and splice site positions.


News

CHANGES IN VERSION 1.7.0

NEW FEATURES

o geneModel, geneList classes added

SIGNIFICANT USER-VISIBLE CHANGES

o (none)

BUG FIXES

o (none)

CHANGES IN VERSION 1.6.0

NEW FEATURES

o getSpliceTable additionally copies transcript_biotype when present

o unifyJuncs counts number of transcripts which are classified as
    nonsense mediated decay

o unifyJuncs now returns refJunctions (i.e. same class as passed object)

o Added extractByGeneId function

SIGNIFICANT USER-VISIBLE CHANGES

o (none)

BUG FIXES

o (none)

CHANGES IN VERSION 1.5.0

NEW FEATURES

o (none)

SIGNIFICANT USER-VISIBLE CHANGES

o New C++ based import of GTF files due to import errors in Ensembl 76 (1.4.2). The attributes table and
related functions are removed.

BUG FIXES

o The new GTF import mechanism is included because the former version produced an error.

CHANGES IN VERSION 1.4.0

NEW FEATURES

o Added a 'unifiedExons' class and 

o Change compilation of source code to C++11 (from C)

SIGNIFICANT USER-VISIBLE CHANGES

o Added support for unification of exonic sites which can be used for counting alignments (reads)

BUG FIXES

o (none)

CHANGES IN VERSION 1.2.8

NEW FEATURES

o Included this NEWS file and a ChangeLog file

o Added a unifyJuncs method: A method for unification of splice sites

o Added overlapJuncs functions: A specialized routine for annotation of splice junctions

SIGNIFICANT USER-VISIBLE CHANGES

o Added support for 'gene' records in gtf file (as introduced by Ensembl 76)

BUG FIXES

o (none)

Reference manual

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install.packages("refGenome")

1.7.7 by ORPHANED, 9 months ago


Browse source code at https://github.com/cran/refGenome


Authors: Wolfgang Kaisers [aut, cre]


Documentation:   PDF Manual  


GPL-2 license


Imports DBI

Depends on methods, doBy, RSQLite


See at CRAN