Learn R Programming

disprose (version 0.1.6)

Discriminating Probes Selection

Description

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., Hner zu Siederdissen C. et al. (2011) ; Camacho C., Coulouris G., Avagyan V. et al. (2009) .

Copy Link

Version

Install

install.packages('disprose')

Monthly Downloads

108

Version

0.1.6

License

GPL-3

Maintainer

Elena Filatova

Last Published

March 18th, 2022

Functions in disprose (0.1.6)

add_adapters

Add adapters to probes
cut_string

Cut string into segments
annotate_probes

Annotate probes
blast.raw

Local BLAST results.
delete_duplicates_DF

Delete rows with duplicated values
count_PhCh

Calculate physical and chemical properties
blast_local

Local BLAST
get_GIs

Get GenInfo Identifier numbers
ann.data

Chlamydia pneumoniae genome annotation.
blast.fill

Local BLAST results with added content.
make_blast_DB

Builds local database for BLAST
get_seq_info

Get NCBI sequence record
fill_blast_result

Complement BLAST result
get_seq_for_DB

Get nucleotide sequences from NCBI
meta.target

Metadata of target Chlamydia pneumoniae's sequences.
summarize_blast_result

Summarize BLAST result
get_GA_files

Read GISAID sequence file
normalize_DF

Normalize variable
read_and_unite_files

Read and unite files
rate_DF

Rate variables
cut_probes

Cut probes
store_in_DB

Store data in SQLite database
read_from_table_file

Read table file
trim_DF

Trim data frame
unite_two_DF

Combine two data frames
unite_NCBI_ac.nums

Assigns master record's id to all project records
make_ids

Create unique identification values
meta.all

Metadata of all available Chlamydia pneumoniae's sequences.