alignment2psl | Take an alignment of targets to chromosome(s) where the... |
blat-package | Methods to import, export and manipulate BLAT result data. |
grow.bed | grow the intervals in a bed file |
import.psl | Import a psl formatted alignment file of queries to targets |
import.ucsc.bed | import a UCSC-format BED file |
make.unique.psl | Convert a PSL alignment data.frame into a minimal 1:1... |
midpoint.bed | Determine the midpoint of an interval |
new.psl | Make a new empty psl table. |
order.psl | determine the order of rows in a psl object, based on... |
psl2bed | Convert a psl alignment from BLAT into a BED alignment. |
psl2coordinates | convert psl file to UCSC-style coordinates |
psl.besthit | obtain the best hit for each query |
pslCalcMilliBad | internal function used to determing a psl alignment score. |
pslIsProtein | is the psl alignment from a protein? |
pslPercentIdentity | calculate the % identity of a psl alignment |
pslPercentIdentity2 | calculate the % identity of a psl alignment V2 |
pslPercentIdentity3 | calculate the % identity of a psl alignment V3 |
pslScore | calculate the score from a psl alignment |
sort.psl | sort a psl file such that each query is together, then by... |
write.psl | Write a psl object out to a psl file. |
write.ucsc.track | Write a psl object to a UCSC-style track |
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