Package: Spec2Annot 1.3.4

Sylvain Dechaumet

Spec2Annot: Annotation of Mass Spectra

Provides a comprehensive suite of functions to efficiently annotate mass spectra data. Motivated by the need for rapid and accurate chemical identification in high-resolution mass spectrometry, it integrates built-in chemical databases and high-performance C++ algorithms. Users can perform mass-to-charge (m/Z) and retention time searches, determine elemental compositions of molecules using heuristic rules, including specific isotopes, and annotate MS2 spectra with structural metrics using configurable chemistry rules.

Authors:Sylvain Dechaumet [aut, cre], Etienne Thevenot [ctb], Eric Venot [rev], Annelaure Damont [ctb], Anaïs Legrand [ctb]

Spec2Annot_1.3.4.tar.gz
Spec2Annot_1.3.4.zip(r-4.7-x86_64)Spec2Annot_1.3.4.zip(r-4.7-arm64)Spec2Annot_1.3.4.zip(r-4.6-x86_64)Spec2Annot_1.3.4.zip(r-4.6-arm64)Spec2Annot_1.3.4.zip(r-4.5-x86_64)
Spec2Annot_1.3.4.tgz(r-4.6-x86_64)Spec2Annot_1.3.4.tgz(r-4.6-arm64)Spec2Annot_1.3.4.tgz(r-4.5-x86_64)Spec2Annot_1.3.4.tgz(r-4.5-arm64)
Spec2Annot_1.3.4.tar.gz(r-4.7-arm64)Spec2Annot_1.3.4.tar.gz(r-4.7-x86_64)Spec2Annot_1.3.4.tar.gz(r-4.6-arm64)Spec2Annot_1.3.4.tar.gz(r-4.6-x86_64)
Spec2Annot_1.3.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
Spec2Annot/json (API)

# Install 'Spec2Annot' in R:
install.packages('Spec2Annot', repos = c('https://odisce.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/odisce/spec2annot/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

cpp

3.40 score 1 stars 33 exports 10 dependencies

Last updated from:f551933f50. Checks:11 OK, 4 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK132
linux-devel-x86_64OK154
source / vignettesOK201
linux-release-arm64OK128
linux-release-x86_64OK155
macos-release-arm64ERROR182
macos-release-x86_64OK381
macos-oldrel-arm64ERROR206
macos-oldrel-x86_64OK254
windows-devel-arm64ERROR352
windows-devel-x86_64OK152
windows-release-arm64ERROR334
windows-release-x86_64OK117
windows-oldrel-x86_64OK121
wasm-releaseOK123

Exports:%>%add_formula_to_annotannot_to_htmlannotate_mzannotate_spectrabrute_force_constCJ1electron_masselement_from_formulafind_compo_from_massfun_generate_ions_from_mzfun_get_ion_listgen_adductgen_formula_from_compogen_ionlistgen_isotopesgen_lossesgen_monochargeget_charge_from_compoget_dbeget_element_from_massget_iso_from_annotget_nruleget_seniormatch_tablesmz_calc_ionmz_from_stringmz_ppmmz_rangemz_vec_aggregatesearch_dbsearch_db_cppstring_from_element

Dependencies:clidata.tablegluelifecyclemagrittrRcpprlangstringistringrvctrs

Readme and manuals

Help Manual

Help pageTopics
Add formula to annotate_mz()add_formula_to_annot
adduct dataAdduct_db
Convert annotation to html stringannot_to_html
Annotate a mass spectrumannotate_mz
Annotate a matrix and return network edgesannotate_spectra
Group m/Z from a vector based on tolerancebrute_force_const
Cross join of two data.tableCJ1
Mono charged ionsdb_monocharge
Return the mass of an electornelectron_mass
Periodic table as a data.tableElement
Get element count from formulaelement_from_formula
Find composition from massfind_compo_from_mass
Calculate the ions databasefun_generate_ions_from_mz
Calculate the ions databasefun_get_ion_list
Generate adduct list from mzgen_adduct
Generate formula from compositiongen_formula_from_compo
Calculate list of targetd ions from neutral mzgen_ionlist
Function to generate isotopes from an exact massgen_isotopes
Generate losses list from mzgen_losses
Function to generate monocharges from an exact massgen_monocharge
Get charge from compositionget_charge_from_compo
Calculate DBE from an elemental compositionget_dbe
Get Element from a massget_element_from_mass
Get isotopes from annotationget_iso_from_annot
Check Nitrogen ruleget_nrule
Get index in rangeget_range
Check Senior theoremsget_senior
ions dataions_database
isotopes dataIsotopes_db
losses dataLosses_db
Match two tablematch_tables
Calculate ion mass using formmz_calc_ion
Calculate mz from a string with signsmz_from_string
Get mass deviation in ppmmz_ppm
Get mass range with ppmmz_range
Group m/Z from a vector based on tolerancemz_vec_aggregate
Search DB egaint EXPsearch_db
Search DB egaint EXP using cpp functionsearch_db_cpp
Spectra examplespectra_full
Spectra examplespectra_ms2
Return a string from an element tablestring_from_element
Valence datavalence_db