BNDBfrequency           Calculates the internal frequencies of BNDB
                        cohorts
DGVfrequency            Frequency calculation of variants compared to
                        DGV.
Decipherfrequency       Frequency calculation of variants compared to
                        Decipher.
FamilyInfoPrep          Mapping Realtionship to unique nanoIDs
OverlapRNAseq           Extract Read counts for genes that overlap SVs.
OverlapRNAseq_solo      Annotating the Overlapping genes with RNAseq
                        expression
RNAseqcombine           Combining the RNAseq reads of family members in
                        a single file.
RNAseqcombine_solo      Combining the RNAseq reads of family members in
                        a single file.
SVexpression_duo_trio   Extract Read counts for genes that are near or
                        overalapping SVs.
SVexpression_solo       Annotating the Overlapping and Non-Overlapping
                        genes with RNAseq expression
buildrunBNBedFiles      Reads BED files to produce bionano Bed files
clinvar_gene            Extracting genes from clinvar database NCBI.
extract_clinvar_mod     Extract the genes and variants related to a
                        genetic disorder from ClinVar
gene_extraction         Extracting genes from gene database NCBI.
gene_list_generation    Extracting genes for phenotype/diseases from
                        NCBI.
gtr_gene                Extracting genes from gtr database NCBI.
internalFrequencyTrio_Duo
                        Calculates the internal frequencies of SV in
                        internal cohorts, for SVMerge
internalFrequency_solo
                        Calculates the internal frequencies of SV in
                        internal cohorts, for SE
makeInternalBNDatabase
                        Merges Solo SV files to one common SV file
mergingSMAP_SE          Merging DLE labelled smaps
mergingSMAP_SVMerge     Merging dual labelled smaps
merging_SE_SVMerge      Merging Dual and DLE, and adding nanotatoR
                        relation ID
nanotatoR               nanotatoR: Annotation package for Bionano Data
nanotatoR_Duo_SVmerge   Annotation and visualisation of Bionano SV, of
                        SVMerge Duo samples.
nanotatoR_SVmerge_Trio
                        Annotation and visualisation of Bionano SV, of
                        DLE Trio samples.
nanotatoR_main_Duo_SE   Annotation and visualisation of Bionano SV, of
                        Single enzyme Duo samples.
nanotatoR_main_Solo_SE
                        Annotation and visualisation of Bionano SV, of
                        DLE Solo samples.
nanotatoR_main_Solo_SVmerge
                        Annotation and visualisation of Bionano SV, of
                        Solo SVMerge samples.
nanotatoR_main_Trio_SE
                        Annotation and visualisation of Bionano SV, of
                        DLE Trio samples.
nonOverlapGenes         Calculates Genes that are near to the SV region
nonOverlapRNAseq        Extract Read counts for genes that are near
                        SVs.
nonOverlapRNAseq_solo   Annotating the Non-Overlapping genes with
                        RNAseq expression
nonOverlappingDNGenes   Extracting terms for genes that overlap SVs
nonOverlappingUPGenes   Extracting terms for genes that overlap SVs
omim_gene               Extracting genes from OMIM database NCBI.
overlapGenes            Calculates Genes that overlap the SV region
overlapnearestgeneSearch
                        Extracts gene information from bed files
overlappingGenes        Extracting terms for genes that overlap SVs
phenoextractHPO_mod     Extract the genes related to a disease or
                        disease alias from HPO database.
readBNBedFiles          Reads Bionano Bedfiles
readSMap                Reads SMAP files to extract information from
                        SVMerge
readSMap_DLE            Reads DLE SMAP files to extract information
reading_GTR             Reading and parsing gtr database.
reading_mim2gene        Reading and parsing OMIM database.
run_bionano_filter_SE_Trio
                        Getting the data from annotated smaps to
                        extract SV information based on type of
                        variants.
run_bionano_filter_SE_duo
                        Getting the data from annotated smaps to
                        extract SV information based on type of
                        variants.
run_bionano_filter_SE_solo
                        Getting the data from annotated smaps to
                        extract SV information based on type of
                        variants.
run_bionano_filter_SVMerge_Trio
                        Getting the data from annotated smaps to
                        extract SV information based on type of
                        variants.
run_bionano_filter_SVMerge_duo
                        Getting the data from annotated smaps to
                        extract SV information based on type of
                        variants.
run_bionano_filter_SVMerge_solo
                        Getting the data from annotated smaps to
                        extract SV information based on type of
                        variants.
