Full genome sequences for Bos taurus (Cow) as provided by UCSC (genome bosTau9
) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau9
, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker
(RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3
, May 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal3
, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker
(RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr3
, Aug. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Sscrofa.UCSC.susScr3
, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker
(RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4
, Oct. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau4
, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker
(RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4
, Nov. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal4
, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker
(RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3
, Aug. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau3
, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker
(RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau6
, Nov. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau6
, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker
(RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
Exposes an annotation databases generated from UCSC by exposing these as TxDb
objects.
Exposes an annotation databases generated from UCSC by exposing these as TxDb
objects.
Exposes an annotation databases generated from UCSC by exposing these as TxDb
objects.
Exposes an annotation databases generated from UCSC by exposing these as TxDb
objects.
This package provides Semantic conventions for OpenTelemetry
.
Package sqlite3 provides interface to SQLite3 databases.
Package sqlite3 provides interface to SQLite3 databases.
This package provides binary input and output for RDF queries.
Exposes an annotation databases generated from UCSC by exposing these as TxDb
objects.
Exposes an annotation databases generated from UCSC by exposing these as TxDb
objects.
iFull
genome sequences for Apis mellifera (Honey Bee) as provided by BeeBase
(assembly4, Feb. 2008) and stored in Biostrings objects.
Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3
, Oct. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac3
, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker
(RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac2
, Jan. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac2
, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker
(RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default. NOTE: In most assemblies available at UCSC, Tandem Repeats Finder repeats were filtered to retain only the repeats with period <= 12. However, the filtering was omitted for this assembly, so the TRF masks contain all Tandem Repeats Finder results.
Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut1
, Jul. 2008) and stored in Biostrings objects. The sequences are the same as in BSgenome.Tguttata.UCSC.taeGut1
, except that each of them has the 2 following masks on top: (1) the mask of assembly gaps (AGAPS mask), and (2) the mask of intra-contig ambiguities (AMB mask). Both masks are "active" by default.
Exposes an annotation databases generated from UCSC by exposing these as TxDb
objects.
Exposes an annotation databases generated from UCSC by exposing these as TxDb
objects.
Exposes an annotation databases generated from UCSC by exposing these as TxDb
objects.