add_adapters |
Add adapters to probes |
ann.data |
Chlamydia pneumoniae genome annotation. |
annotate_probes |
Annotate probes |
blast.fill |
Local BLAST results with added content. |
blast.raw |
Local BLAST results. |
blast_local |
Local BLAST |
count_GC |
Calculate physical and chemical properties |
count_MFE |
Calculate physical and chemical properties |
count_PhCh |
Calculate physical and chemical properties |
count_REP |
Calculate physical and chemical properties |
count_TM |
Calculate physical and chemical properties |
cut_probes |
Cut probes |
cut_string |
Cut string into segments |
delete_AcNum_version |
Complement BLAST result |
delete_duplicates_DF |
Delete rows with duplicated values |
delete_from_DB |
Store data in SQLite database |
fill_blast_result |
Complement BLAST result |
fill_blast_results |
Complement BLAST result |
get_GA_files |
Read GISAID sequence file |
get_GIs |
Get GenInfo Identifier numbers |
get_GIs_fix |
Get GenInfo Identifier numbers |
get_seq_for_DB |
Get nucleotide sequences from NCBI |
get_seq_for_DB_fix |
Get nucleotide sequences from NCBI |
get_seq_info |
Get NCBI sequence record |
get_seq_info_fix |
Get NCBI sequence record |
index_DB |
Store data in SQLite database |
info_listtodata |
Get NCBI sequence record |
list_DB |
Store data in SQLite database |
make_blast_DB |
Builds local database for BLAST |
make_ids |
Create unique identification values |
meta.all |
Metadata of all available Chlamydia pneumoniae's sequences. |
meta.target |
Metadata of target Chlamydia pneumoniae's sequences. |
normalize_DF |
Normalize variable |
rate_DF |
Rate variables |
read_and_unite_files |
Read and unite files |
read_from_DB |
Store data in SQLite database |
read_from_table_file |
Read table file |
store_in_DB |
Store data in SQLite database |
summarize_blast_result |
Summarize BLAST result |
trim_DF |
Trim data frame |
unite_NCBI_ac.nums |
Assigns master record's id to all project records |
unite_two_DF |
Combine two data frames |
write_to_DB |
Store data in SQLite database |