Files in VilainLab/nanotatoR
Next generation structural variant annotation and classification
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/DGV_extraction.r
R/DecipherExtraction.r
R/InternalFrequency_SE.r
R/InternalFrequency_SVMerge.r
R/OverlappingGenes.r
R/RNASEQ_Analysis_Duo_Trio_SVMerge_SE.r
R/RNASEQ_Analysis_solo_SVMerge_SE.r
R/cohortDB_comp.r
R/extractclinvar_mod.r
R/filter_overlapping_non_overlapping.r
R/filterread_Duo_SE.r
R/filterread_Duo_SVMerge.r
R/filterread_SE_Trio.r
R/filterread_Solo_SE.r
R/filterread_Solo_SVMerge.r
R/filterread_Trio_SVMerge.r
R/gene_extract.r
R/mainAnnotator_SVMerge_Trio.r
R/mergesmap_SVMerge_SE.R
R/nanotatoR.r
R/nanotatoRmain_Duo_SVMerge.r
R/nanotatoRmain_SE_Duo.r
R/nanotatoRmain_Solo_SE.r
R/nanotatoRmain_Solo_SVMerge.r
R/nanotatoRmain_Trio_SE.r
R/phenoextract_mod.r
README.Rmd
inst/extdata/Bionano_config/current_ctrl_dup_hg19_anonymize.txt
inst/extdata/Bionano_config/current_ctrl_ins_del_hg19_anonymize.txt
inst/extdata/Bionano_config/current_ctrl_inv_hg19_anonymize.txt
inst/extdata/Bionano_config/current_ctrl_trans_hg19_anonymize.txt
inst/extdata/GM24385_Ason_DLE1_VAP_trio5.smap
inst/extdata/GRCh37_hg19_variants_2016-05-15.txt
inst/extdata/HomoSapienGRCH19_lift37.bed
inst/extdata/HomoSapienGRCH19_lift37_BN.bed
inst/extdata/NA12878_DLE1_VAP_solo5.smap
inst/extdata/NA12878_P_Blood_S1.genes.results
inst/extdata/NA12878_Q.S_VAP_SVmerge_solo5.txt
inst/extdata/Sample_index.csv
inst/extdata/SoloFile/GM24143_Amother_DLE1_VAP_solo5.smap
inst/extdata/SoloFile/GM24149_Afather_DLE1_VAP_solo5.smap
inst/extdata/SoloFile/GM24385_Ason_DLE1_VAP_solo5.smap
inst/extdata/SoloFile/NA12878_DLE1_VAP_solo5.smap
inst/extdata/SoloFile/NA12878_Q.S_VAP_SVmerge_solo5.txt
inst/extdata/gtrDatabase.txt
inst/extdata/localPDB/gene_condition_source_id
inst/extdata/localPDB/phenotype_annotation.tab
inst/extdata/localPDB/phenotype_to_genes.txt
inst/extdata/localPDB/variant_summary.txt.gz
inst/extdata/mim2gene.txt
inst/extdata/nanotatoRControl.txt
inst/extdata/nanotatoR_control_sample_codes.csv
inst/extdata/nanotatoR_sample_codes.csv
inst/extdata/population_cnv.txt
inst/scripts/data.r
man/BNDBfrequency.Rd
man/DGVfrequency.Rd
man/Decipherfrequency.Rd
man/FamilyInfoPrep.Rd
man/OverlapRNAseq.Rd
man/OverlapRNAseq_solo.Rd
man/RNAseqcombine.Rd
man/RNAseqcombine_solo.Rd
man/SVexpression_duo_trio.Rd
man/SVexpression_solo.Rd
man/buildrunBNBedFiles.Rd
man/clinvar_gene.Rd
man/extract_clinvar_mod.Rd
man/gene_extraction.Rd
man/gene_list_generation.Rd
man/gtr_gene.Rd
man/internalFrequencyTrio_Duo.Rd
man/internalFrequency_solo.Rd
man/makeInternalBNDatabase.Rd
man/mergingSMAP_SE.Rd
man/mergingSMAP_SVMerge.Rd
man/merging_SE_SVMerge.Rd
man/nanotatoR.Rd
man/nanotatoR_Duo_SVmerge.Rd
man/nanotatoR_SVmerge_Trio.Rd
man/nanotatoR_main_Duo_SE.Rd
man/nanotatoR_main_Solo_SE.Rd
man/nanotatoR_main_Solo_SVmerge.Rd
man/nanotatoR_main_Trio_SE.Rd
man/nonOverlapGenes.Rd
man/nonOverlapRNAseq.Rd
man/nonOverlapRNAseq_solo.Rd
man/nonOverlappingDNGenes.Rd
man/nonOverlappingUPGenes.Rd
man/omim_gene.Rd
man/overlapGenes.Rd
man/overlapnearestgeneSearch.Rd
man/overlappingGenes.Rd
man/phenoextractHPO_mod.Rd
man/readBNBedFiles.Rd
man/readSMap.Rd
man/readSMap_DLE.Rd
man/reading_GTR.Rd
man/reading_mim2gene.Rd
man/run_bionano_filter_SE_Trio.Rd
man/run_bionano_filter_SE_duo.Rd
man/run_bionano_filter_SE_solo.Rd
man/run_bionano_filter_SVMerge_Trio.Rd
man/run_bionano_filter_SVMerge_duo.Rd
man/run_bionano_filter_SVMerge_solo.Rd
nanotatoR.Rproj
tests/testthat.R
tests/testthat/test_entrez_extract.R
vignettes/nanotatoR.Rmd
