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