Package: disprose 0.1.6

Elena Filatova

disprose: Discriminating Probes Selection

Set of tools for molecular probes selection and design of a microarray, e.g. the assessment of physical and chemical properties, blast performance, selection according to sensitivity and selectivity. Methods used in package are described in: Lorenz R., Stephan H.B., Höner zu Siederdissen C. et al. (2011) <doi:10.1186/1748-7188-6-26>; Camacho C., Coulouris G., Avagyan V. et al. (2009) <doi:10.1186/1471-2105-10-421>.

Authors:Elena Filatova [aut, cre], Oleg Utkin [ctb], Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Russia [fnd]

disprose_0.1.6.tar.gz
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disprose.pdf |disprose.html✨
disprose/json (API)
NEWS

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

Peer review:

Datasets:
  • ann.data - Chlamydia pneumoniae genome annotation.
  • blast.fill - Local BLAST results with added content.
  • blast.raw - Local BLAST results.
  • meta.all - Metadata of all available Chlamydia pneumoniae's sequences.
  • meta.target - Metadata of target Chlamydia pneumoniae's sequences.

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 250 downloads 36 exports 0 dependencies

Last updated 3 years agofrom:fe1db5a884. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 13 2024
R-4.5-linuxNOTEDec 13 2024

Exports:add_adaptersannotate_probesblast_localcount_GCcount_MFEcount_PhChcount_REPcount_TMcut_probescut_stringdelete_AcNum_versiondelete_duplicates_DFdelete_from_DBfill_blast_resultsget_GA_filesget_GIsget_GIs_fixget_seq_for_DBget_seq_for_DB_fixget_seq_infoget_seq_info_fixindex_DBinfo_listtodatalist_DBmake_blast_DBmake_idsnormalize_DFrate_DFread_and_unite_filesread_from_DBread_from_table_filesummarize_blast_resulttrim_DFunite_NCBI_ac.numsunite_two_DFwrite_to_DB

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Add adapters to probesadd_adapters
Chlamydia pneumoniae genome annotation.ann.data
Annotate probesannotate_probes
Local BLASTblast_local
Local BLAST results with added content.blast.fill
Local BLAST results.blast.raw
Calculate physical and chemical propertiescount_GC count_MFE count_PhCh count_REP count_TM
Cut probescut_probes
Cut string into segmentscut_string
Delete rows with duplicated valuesdelete_duplicates_DF
Complement BLAST resultdelete_AcNum_version fill_blast_result fill_blast_results
Read GISAID sequence fileget_GA_files
Get GenInfo Identifier numbersget_GIs get_GIs_fix
Get nucleotide sequences from NCBIget_seq_for_DB get_seq_for_DB_fix
Get NCBI sequence recordget_seq_info get_seq_info_fix info_listtodata
Builds local database for BLASTmake_blast_DB
Create unique identification valuesmake_ids
Metadata of all available Chlamydia pneumoniae's sequences.meta.all
Metadata of target Chlamydia pneumoniae's sequences.meta.target
Normalize variablenormalize_DF
Rate variablesrate_DF
Read and unite filesread_and_unite_files
Read table fileread_from_table_file
Store data in SQLite databasedelete_from_DB index_DB list_DB read_from_DB store_in_DB write_to_DB
Summarize BLAST resultsummarize_blast_result
Trim data frametrim_DF
Assigns master record's id to all project recordsunite_NCBI_ac.nums
Combine two data framesunite_two_DF