Files in arcolombo/TxDbLite
Lightweight SQLite-based annotation classes/packages for use with arkas
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/ArrayControlDbLite.R
R/EnsDbLite.R
R/ErccDbLite.R
R/RepDbLite.R
R/TxDbLite-class.R
R/TxDbLite-methods.R
R/TxDbLite.R
R/chrs.R
R/createAnnotationPackage.R
R/data.R
R/ensDbLiteFromFasta.R
R/erccDbLiteFromFasta.R
R/fetchFromEnsembl.R
R/findDupes.R
R/getAnnotationType.R
R/getDupeSeq.R
R/getGCcontent.R
R/getHugoCache.R
R/getMostRecentCacheBuild.R
R/getReactomeCache.R
R/getReactomeUrl.R
R/indexIfNoneFound.R
R/loadReactome.R
R/makeArrayControlDbLitePkg.R
R/makeEnsDbLitePkg.R
R/makeErccDbLitePkg.R
R/makeRepDbLitePkg.R
R/mapHugo.R
R/mapReactomeSets.R
R/mapToReactome.R
R/miDbLite.R
R/reactomeSets.R
R/repDbLiteFromFasta.R
R/repDbLiteFromMouseFasta.R
R/spikeinDbLiteFromFasta.R
R/str2vec.R
R/strpop.R
R/strpush.R
R/strshift.R
R/strunshift.R
R/utils.R
README.md
data/ERCC_annotated.rda
data/ensemblToReactome.rda
data/ensembl_biotypes.rda
data/hugoCache.rda
data/mouseCopyNumber.mm10.rda
data/mouse_repeat_biotypes.rda
data/reactomeCache.rda
data/reactomePathways.rda
data/repeatCopyNumber.hg19.rda
data/repeat_biotypes.rda
data/supportedOrganismsForTxDbLite.rda
data/unannotatedTranscript.rda
demo/00Index
demo/annotateRepeats.R
demo/bestMatch.R
demo/findRepBaseDupes.R
demo/repBaseClass.R
demo/repBaseToRmsk.R
demo/repPrep.R
demo/repeats.R
demo/vegaBioClass.R
inst/arraycontroldblite/DESCRIPTION
inst/arraycontroldblite/NAMESPACE
inst/arraycontroldblite/R/zzz.R
inst/arraycontroldblite/man/package.Rd
inst/bin/Ensembl2Reactome_All_Levels.txt
inst/bin/extractAllLevels.sh
inst/ensdblite/DESCRIPTION
inst/ensdblite/NAMESPACE
inst/ensdblite/R/zzz.R
inst/ensdblite/man/package.Rd
inst/erccdblite/DESCRIPTION
inst/erccdblite/NAMESPACE
inst/erccdblite/R/zzz.R
inst/erccdblite/man/package.Rd
inst/extdata/DE_repeats.csv
inst/extdata/Drosophila_melanogaster.BDGP6.ncrna.fa.gz
inst/extdata/ERCC.fa.gz
inst/extdata/FIsInGene_031516_with_annotations.txt
inst/extdata/Homo_sapiens.GRCh38.81.ncrna.fa.gz
inst/extdata/Homo_sapiens.RepBase.20_05.merged.fa.gz
inst/extdata/Homo_sapiens.RepBase.20_05.merged.fa.gz.fai
inst/extdata/RepDbLite.Hsapiens.2005.sqlite
inst/extdata/reactome/Ensembl2Reactome.txt.gz
inst/extdata/reactome/ReactomePathways.txt.gz
inst/extdata/reactome/caenorhabditis_elegans.interactions.txt.gz
inst/extdata/reactome/danio_rerio.interactions.txt.gz
inst/extdata/reactome/drosophila_melanogaster.interactions.txt.gz
inst/extdata/reactome/homo_sapiens.interactions.txt.gz
inst/extdata/reactome/mus_musculus.interactions.txt.gz
inst/extdata/reactome/rattus_norvegicus.interactions.txt.gz
inst/repdblite/DESCRIPTION
inst/repdblite/NAMESPACE
inst/repdblite/R/zzz.R
inst/repdblite/man/package.Rd
man/ArrayControlDbLite.Rd
man/ERCC_annotated.Rd
man/EnsDbLite.Rd
man/ErccDbLite.Rd
man/RepDbLite.Rd
man/TxDbLite-class.Rd
man/TxDbLite.Rd
man/chrs.Rd
man/createAnnotationPackage.Rd
man/ensDbLiteFromFasta.Rd
man/ensemblToReactome.Rd
man/ensembl_biotypes.Rd
man/erccDbLiteFromFasta.Rd
man/fetchFromEnsembl.Rd
man/findDupes.Rd
man/getAnnotationType.Rd
man/getDupeSeq.Rd
man/getGCcontent.Rd
man/getHugoCache.Rd
man/getMostRecentCacheBuild.Rd
man/getReactomeCache.Rd
man/getReactomeUrl.Rd
man/hugoCache.Rd
man/indexIfNoneFound.Rd
man/loadReactome.Rd
man/makeArrayControlLitePkg.Rd
man/makeEnsDbLitePkg.Rd
man/makeErccDbLitePkg.Rd
man/makeRepDbLitePkg.Rd
man/mapHugo.Rd
man/mapReactomeSets.Rd
man/mapToReactome.Rd
man/mouse_repeat_biotypes.Rd
man/reactomeCache.Rd
man/reactomePathways.Rd
man/reactomeSets.Rd
man/repDbLiteFromFasta.Rd
man/repDbLiteFromMouseFasta.Rd
man/repDbLiteMetadata.Rd
man/repeat_biotypes.Rd
man/spikeinDbLiteFromFasta.Rd
man/str2vec.Rd
man/strpop.Rd
man/strpush.Rd
man/strshift.Rd
man/strunshift.Rd
man/supportedOrganismsForTxDbLite.Rd
man/unannotatedTranscript.Rd
man/utils.Rd
vignettes/makeTxDbLiteAnnotationLibrary.Rmd
vignettes/makeTxDbLiteAnnotationLibrary.html
