Files in SimonSchafferer/short-ncrna-annotation
Non-coding RNA annotation package
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/EnsemblAnnotation.R
R/GRangesBasedAnnotation.R
R/ModifyUCSCEnsemblGTF.R
R/RangedAnnotation.R
R/RefSeqUCSCAnnotation.R
R/SequenceBasedAnnotation.R
R/UtilityFunctions.R
README.md
data/ModifyEnsemblAnnotation.py
data/testAnnotation.bed~
data/testData.bed~
data/testInterestCand.bed~
demo/.gitignore
inst/resources/TestData/TestEnsemblGene.R
inst/resources/TestData/inSeq.fsa
inst/resources/TestData/testAnnotation.bed
inst/resources/TestData/testFastadb.fsa
inst/resources/TestData/testFastadb.nhr
inst/resources/TestData/testFastadb.nin
inst/resources/TestData/testFastadb.nsq
inst/resources/TestData/testInterestCand.bed
inst/resources/TestData/testNewBlast
inst/resources/TestData/testOldBlast
inst/resources/ensembl/ensembl_gtf_hg19.rda
inst/resources/ensembl/ensembl_gtf_hg38_78.rda
inst/resources/ensembl/ensembl_gtf_v67_mm9.rda
inst/resources/ensembl/ensembl_gtf_v75_mm10.rda
inst/resources/frnadb/MusMusculus/paramtersForBlasting
inst/resources/frnadb/Mus_musculus.fasta.fai
inst/resources/frnadb/Mus_musculus.fasta.nhr
inst/resources/frnadb/Mus_musculus.fasta.nin
inst/resources/frnadb/Mus_musculus.fasta.nsq
inst/resources/ucsc/refseqGenes_gtf_ucsc_hg19.rda
inst/resources/ucsc/refseqGenes_gtf_ucsc_mm10.rda
inst/resources/ucsc/refseqGenes_gtf_ucsc_mm9.rda
inst/shortNCRNAannotation.png
man/EnsemblAnnotation-class.Rd
man/EnsemblAnnotation.Rd
man/GRangesBasedAnnotation-class.Rd
man/GRangesBasedAnnotation.Rd
man/NcbiBlastAnnotation-class.Rd
man/NcbiBlastAnnotation-method.Rd
man/RangedAnnotation-class.Rd
man/RangedAnnotation.Rd
man/RefSeqUCSCAnnotation-class.Rd
man/RefSeqUCSCAnnotation.Rd
man/SequenceBasedAnnotation-class.Rd
man/annotName-method.Rd
man/annotationGR-method.Rd
man/annotationL-method.Rd
man/annotationMap-method.Rd
man/annotationSummary-method.Rd
man/calculateAlignmentCoverageTwoGRanges.Rd
man/convertRangesToDF-method.Rd
man/createRObject_gtf.Rd
man/executeAnnotation-method.Rd
man/feature_annotation_Function-method.Rd
man/getAnnotationByID-method.Rd
man/getFlatTable-method.Rd
man/importRangedAnnotation-method.Rd
man/initialize-RangedAnnotation-method.Rd
man/initialize-SequenceBasedAnnotation-method.Rd
man/inputGR-method.Rd
man/loadLibraryGloballyAs.Rd
man/loadLibraryLocallyAs.Rd
man/protein_coding_AnnotationFunction-method.Rd
short-ncrna-annotation.Rproj
