Package: igblastr 1.3.6
Hervé Pagès
igblastr: User-friendly R Wrapper to IgBLAST
The igblastr package provides functions to conveniently install and use a local IgBLAST installation from within R. The package also includes a set of built-in IgBLAST-compatible germline databases from OGRDB, the AIRR Community’s Open Germline Receptor Database, for various organisms. It provides functions to create additional IgBLAST-compatible germline databases using reference sequences retrieved from IMGT/V-QUEST or local FASTA files supplied by the user. When possible, annotations for the V and J alleles in a new germline database are automatically computed and added to the database, so they can be used as replacements for the internal and auxiliary data shipped with IgBLAST. IgBLAST is described at <https://pubmed.ncbi.nlm.nih.gov/23671333/>. IgBLAST web interface: <https://www.ncbi.nlm.nih.gov/igblast/>. OGRDB: <https://ogrdb.airr-community.org/>. IMGT/V-QUEST download site: <https://www.imgt.org/download/V-QUEST/>.
Authors:
igblastr_1.3.6.tar.gz
igblastr_1.3.6.zip(r-4.7)igblastr_1.3.6.zip(r-4.6)igblastr_1.3.6.zip(r-4.5)
igblastr_1.3.6.tgz(r-4.6-any)igblastr_1.3.6.tgz(r-4.5-any)
igblastr_1.3.6.tar.gz(r-4.7-any)igblastr_1.3.6.tar.gz(r-4.6-any)
igblastr_1.3.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
igblastr/json (API)
NEWS
| # Install 'igblastr' in R: |
| install.packages('igblastr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hyrienlab/igblastr/issues
On BioConductor:igblastr-1.3.5(bioc 3.24)igblastr-1.2.5(bioc 3.23)
immunologyimmunogeneticsimmunooncologycellbiologybioconductor-package
Last updated from:a3152c5834. Checks:2 WARNING, 4 NOTE, 2 OK, 2 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 181 | ||
| linux-devel-x86_64 | NOTE | 635 | ||
| source / vignettes | OK | 335 | ||
| linux-release-x86_64 | NOTE | 585 | ||
| macos-release-arm64 | NOTE | 561 | ||
| macos-oldrel-arm64 | ERROR | 238 | ||
| windows-devel | NOTE | 760 | ||
| windows-release | WARNING | 696 | ||
| windows-oldrel | ERROR | 419 | ||
| wasm-release | OK | 138 |
Exports:allele2geneaugment_germline_db_Daugment_germline_db_Jaugment_germline_db_Vbcr_browsercombine_c_region_dbscombine_germline_dbscompute_auxdatacompute_germline_db_auxdatacompute_imgt_intdatacompute_V_gene_delineationsdownload_IMGT_germline_sequencesdownload_OGRDB_germline_jsondownload_OGRDB_germline_sequencesdownload_paired_OAS_unitsextract_auxdata_from_ogrdb_jsonextract_codonsextract_intdata_from_ogrdb_jsonextract_metadata_from_OAS_unitsextract_sequences_from_paired_OAS_dfextract_sequences_from_paired_OAS_unitsget_auxdata_pathget_igblast_auxiliary_dataget_igblast_rootget_intdata_pathhas_igblastigblast_buildigblast_infoigblastnigblastn_helpigblastn_versionigbrowserigdata_infoIMGT_is_upinfer_cdr3_ends_via_fwr4_comparisonsinstall_custom_germline_dbinstall_igblastinstall_IMGT_c_region_dbinstall_IMGT_germline_dbJ_allele_has_stop_codonlist_c_region_dbslist_germline_dbslist_igblast_organismslist_IMGT_organismslist_IMGT_releaseslist_outfmt7_specifierslist_paired_OAS_studieslist_paired_OAS_unitsload_auxdataload_c_region_dbload_c_region_sequencesload_germline_dbload_germline_sequencesload_igblast_auxiliary_dataload_intdatamakeblastdb_versionOAS_is_upparse_imgt_fasta_headersparse_outfmt7print_J_allelesprint.alignment_summaryprint.auxdata_md5sum_dfprint.c_region_dbs_dfprint.fmt7footerprint.fmt7recordprint.germline_dbs_dfprint.hit_tableprint.igblast_infoprint.igblastn_raw_outputprint.igdata_infoprint.outfmt7_specifiersprint.query_detailsprint.subregion_sequence_detailsprint.VDJ_junction_detailsprint.VDJ_rearrangement_summaryqseqidqseqid.fmt7recordqseqid.query_detailsread_auxdataread_igblastn_AIRR_outputread_igblastn_fmt7_outputread_ndm_dataread_OAS_csvread_OAS_csv_metadataremove_gapsreset_c_region_dbsreset_germline_dbsreset_live_igdatarm_c_region_dbrm_germline_dbsame_alleles_annotset_igblast_rootshow_intdata_disagreementssummary.query_detailstabulate_deletionstabulate_insertionstabulate_mismatchestime_since_live_igdata_last_checkedtranslate_codonstranslate_fwr4translate_J_allelestranslate_V_allelesupdate_live_igdatause_c_region_dbuse_germline_dbV_allele_has_stop_codonV_genes_with_varying_fwrcdr_boundariesvalidate_ndm_rowswrite_auxdatawrite_ndm_data
Dependencies:askpassBiocGenericsBiostringsclicrayoncurlgenericsGenomeInfoDbgluehttrIRangesjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigR.methodsS3R.ooR.utilsR6rlangrvestS4VectorsselectrSeqinfostringistringrsystibbleUCSC.utilsutf8vctrsxml2xtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Go from germline gene allele names to germline gene names | allele2gene |
| Add novel gene alleles to a germline db | augment_germline_db augment_germline_db_D augment_germline_db_J augment_germline_db_V |
| Read/write IgBLAST auxiliary data files | auxdata-IO auxdata_IO read_auxdata write_auxdata |
| Access IgBLAST auxiliary data | auxdata auxdata-utils auxdata_utils compute_germline_db_auxdata get_auxdata_path get_igblast_auxiliary_data load_auxdata load_igblast_auxiliary_data |
| Combine two existing germline dbs | combine_c_region_dbs combine_germline_dbs |
| Compute IgBLAST auxiliary data | compute_auxdata infer_cdr3_ends_via_fwr4_comparisons |
| Compute V gene delineations | compute_imgt_intdata compute_V_gene_delineations |
| Download germline sequences from IMGT | download_IMGT_germline_sequences IMGT_is_up list_IMGT_organisms list_IMGT_releases |
| Download AIRR-C JSON files from OGRDB | download_OGRDB_germline_json extract_auxdata_from_ogrdb_json extract_intdata_from_ogrdb_json |
| Download germline sequences from OGRDB | download_OGRDB_germline_sequences |
| Control IgBLAST installation to use | get_igblast_root set_igblast_root |
| Check IgBLAST used by igblastr | has_igblast igblastn_version igblast_build igblast_info list_igblast_organisms makeblastdb_version print.igblast_info |
| Use an external IgBLAST installation | IGBLAST_ROOT |
| BLAST for BCR/Ig and TCR sequences | igblastn igblastn_help print.igblastn_raw_output |
| Turn "Usage Reporting" on or off | BLAST_USAGE_REPORT igblastr_usage_report Usage_report usage_report Usage_reporting usage_reporting |
| Display annotated BCR sequences in a browser | bcr_browser igbrowser |
| Install a germline db from user-supplied gene allele sequences | install_custom_germline_db |
| Install IgBLAST | install_igblast |
| Install a germline db from IMGT | install_IMGT_c_region_db install_IMGT_germline_db |
| Access IgBLAST internal data | get_intdata_path intdata intdata-utils intdata_utils load_intdata show_intdata_disagreements V_genes_with_varying_fwrcdr_boundaries |
| Basic inspection of J allele sequences | J_alleles-inspect J_alleles_inspect J_allele_has_stop_codon print_J_alleles translate_fwr4 translate_J_alleles |
| List cached C-region dbs | list_c_region_dbs print.c_region_dbs_df rm_c_region_db |
| List cached germline dbs | list_germline_dbs print.germline_dbs_df rm_germline_db |
| Read/write "ndm" files | ndm_data-IO ndm_data_IO read_ndm_data same_alleles_annot validate_ndm_rows write_ndm_data |
| Download and manipulate OAS data | download_paired_OAS_units extract_metadata_from_OAS_units extract_sequences_from_paired_OAS_df extract_sequences_from_paired_OAS_units list_paired_OAS_studies list_paired_OAS_units OAS-utils OAS_is_up OAS_utils read_OAS_csv read_OAS_csv_metadata |
| Parse IMGT FASTA headers | parse_imgt_fasta_headers |
| igblastn output format 19 (AIRR format) | read_igblastn_AIRR_output |
| igblastn output format 7 | fmt7-utils fmt7_utils list_outfmt7_specifiers outfmt7-utils outfmt7_utils parse_outfmt7 print.alignment_summary print.fmt7footer print.fmt7record print.hit_table print.outfmt7_specifiers print.query_details print.subregion_sequence_details print.VDJ_junction_details print.VDJ_rearrangement_summary qseqid qseqid.fmt7record qseqid.query_details read_igblastn_fmt7_output summary.query_details |
| Reset the cached C-region dbs | reset_c_region_dbs |
| Reset the cached germline dbs | reset_germline_dbs |
| Summarize mismatches and indels between query and germline sequences | summarizeMismatches tabulate_deletions tabulate_insertions tabulate_mismatches |
| Extract and translate codons from a set of DNA sequences | extract_codons remove_gaps translate_codons |
| Update and manage IgBLAST auxiliary and internal data | igdata_info live_igdata print.auxdata_md5sum_df print.igdata_info reset_live_igdata time_since_live_igdata_last_checked update_live_igdata |
| Select cached C-region db to use with igblastn() | load_c_region_db load_c_region_sequences use_c_region_db |
| Select cached germline db to use with igblastn() | load_germline_db load_germline_sequences use_germline_db |
| Basic inspection of V allele sequences | translate_V_alleles V_alleles-inspect V_alleles_inspect V_allele_has_stop_codon |
