Ncbi-Entrez-Direct
- accn-at-a-time(1) at-a-time - parse an input file into biological identifiers
- align-columns(1) columns - align the columns of tab-delimited input
- amino-acid-composition(1) acid-composition - report amino acid composition
- archive-pmc(1) pmc - maintain a local NCBI PubMed Central archive
- archive-pubmed(1) maintain a local NCBI PubMed archive
- asn2ref(1) produce Reference Index (CITATION) XML from Seq-entry ASN.1
- between-two-genes(1) two-genes - select a range of tab-delimited lines
- blst2tkns(1) tokenize XML-formatted magicblast output
- cit2pmid(1) find candidate NCBI PubMed identifiers for a citation
- combine-uid-lists(1) uid-lists - merge numerical lists
- csv2xml(1) transmute to XML
- custom-index(1) index - add a custom index to a local NCBI Entrez archive
- difference-uid-lists(1) uid-lists - compute symmetric difference of two numerical lists
- disambiguate-nucleotides(1) print all corresponding concrete sequences
- download-ncbi-data(1) ncbi-data - download specific data from NCBI's FTP site
- download-ncbi-software(1) ncbi-software - download executables from NCBI's FTP site
- download-pmc(1) pmc - download an NCBI PubMed Central archive dump
- download-pubmed(1) pubmed - download an NCBI PubMed archive dump
- download-sequence(1) sequence - download NCBI ASN.1 biological sequence batches
- ds2pme(1) convert PubMed DocumentSummary XML to Pubmed-entry ASN.1 text
- edict(1) HTTP server for EDirect local PubMed archive and search system
- efetch.ncbi(1) retrieve results from an NCBI Entrez search
- efilter(1) filter and/or sort NCBI Entrez search results
- einfo.ncbi(1) look up general NCBI Entrez database information
- elink(1) look up related NCBI Entrez records
- epost(1) upload a batch of NCBI Entrez record identifiers
- esample(1) print a sample document for use with NCBI Entrez Direct
- esearch(1) search an NCBI Entrez database
- esummary(1) retrieve results from an NCBI Entrez search
- exclude-uid-lists(1) uid-lists - compute the set difference of two numerical lists
- expand-current(1) current - expand a local NCBI PubMed archive
- fetch-pmc(1) pmc - fetch records from a local NCBI PubMed Central archive by UID
- fetch-pubmed(1) pubmed - fetch records from a local NCBI PubMed archive by UID
- filter-columns(1) columns - filter a tab-delimited table per custom criteria
- filter-stop-words(1) stop-words - filter out unindexed NCBI Entrez words
- find-in-gene(1) in-gene - list names of genes overlapping a range
- fuse-ranges(1) ranges - consolidate adjacent or overlapping integral ranges
- fuse-segments(1) segments - consolidate adjacent or overlapping integral segments
- gbf2ref(1) transmute to XML
- gbf2xml(1) transmute to XML
- gene2range(1) simplify NCBI Entrez gene document summaries for find-in-gene
- hgvs2spdi(1) transform genomic variation data from HGVS to SPDI format
- index-extras(1) extras - populate and index local BioConcepts, GeneRifs, and theme data
- index-pubmed(1) maintain a local NCBI PubMed archive
- intersect-uid-lists(1) uid-lists - compute the intersection of two numerical lists
- join-into-groups-of(1) into-groups-of - join input words into N-word groups
- json2xml(1) transmute to XML
- nquire(1) query NCBI Entrez Utilities, other parameter-based web services, or FTP
- phrase-search(1) search - search an indexed local NCBI PubMed archive
- pm-collect(1) collect - collect records from a local NCBI PubMed archive
- pm-prepare(1) prepare - prepare directories to hold a local NCBI PubMed archive
- pm-refresh(1) refresh - refresh versioned NCBI PubMed records
- pma2pme(1) convert PubmedArticle XML to Pubmed-entry ASN.1 text
- print-columns(1) columns - transform lines of a tab-delimited table
- rchive(1) work with a local archive of Entrez document summaries
- ref2pmid(1) match PubMed citations in Reference Index XML
- reorder-columns(1) columns - reorder columns of a tab-delimited file
- run-ncbi-converter(1) ncbi-converter - Run a converter from NCBI's FTP site
- scn2xml(1) transmute to XML
- skip-if-file-exists(1) if-file-exists - filter out lines naming existing files
- snp2hgvs(1) extract HGVS records from Entrez SNP document summaries
- snp2tbl(1) present Entrez SNP document summaries in tabular form
- sort-table(1) table - sort a tab-delimited table
- sort-uniq-count-rank(1) print line frequencies
- sort-uniq-count(1) print line frequencies
- spdi2tbl(1) present NCBI SPDI-format SNP data in tabular form
- split-at-intron(1) at-intron - summarize genomic insertions from blst2tkns output
- stream-pubmed(1) pubmed - dump a local NCBI PubMed archive in compressed form
- tbl2prod(1) pair modified mRNA and protein sequences for SNP data
- tbl2xml(1) transmute to XML
- theme-aliases(1) aliases - establish bash aliases for some phrase-search commands
- transmute(1) transform data, particularly within NCBI Entrez Direct
- uniq-table(1) table - print columns taking on multiple values
- word-at-a-time(1) at-a-time - parse an input file into alphanumeric words
- xml2fsa(1) print FASTA sequence data for INSDSeq XML
- xml2tbl(1) transform INSDSeq XML into an NCBI five-column feature table
- xy-plot(1) plot - produce and display a line graph