📦 ncbi-entrez-direct

A

• accn-at-a-time(1)parse an input file into biological identifiers✨
• align-columns(1)align the columns of tab-delimited input✨
• amino-acid-composition(1)report amino acid composition✨
• archive-nihocc(1)maintain a local NIH Open Citation Collection archive✨
• archive-nlmnlp(1)maintain a local BioConcepts (PubTator) and GeneRifs archive✨
• archive-nmcds(1)maintain a local NCBI RefSeq human mRNA archive✨
• archive-pids(1)maintain a local NCBI PubMed / PubMed Central ID map✨
• archive-pmc(1)maintain a local NCBI PubMed Central archive✨
• archive-pubmed(1)maintain a local NCBI PubMed archive✨
• archive-taxonomy(1)maintain a local NCBI taxonomy archive✨
• args2slice(1)format arguments as a literal Go string array✨
• asn2ref(1)produce Reference Index (CITATION) XML from Seq-entry ASN.1✨

B

• between-two-genes(1)select a range of tab-delimited lines✨
• blst2tkns(1)tokenize XML-formatted magicblast output✨
• bsmp2info(1)convert NCBI BioSample docsum XML to BioSampleInfo XML✨

C

• cit2pmid(1)find candidate NCBI PubMed identifiers for a citation✨
• combine-uid-lists(1)merge numerical lists✨
• csv2xml(1)XMLify✨
• custom-index(1)add a custom index to a local NCBI Entrez archive✨

D

• difference-uid-lists(1)compute symmetric difference of two numerical lists✨
• disambiguate-nucleotides(1)print all corresponding concrete sequences✨
• download-flatfile(1)download consolidated NCBI GenBank flatfiles.✨
• download-ncbi-data(1)download specific data from NCBI's FTP site✨
• download-ncbi-software(1)download executables from NCBI's FTP site✨
• download-pmc(1)download an NCBI PubMed Central archive dump✨
• download-pubmed(1)download an NCBI PubMed archive dump✨
• download-sequence(1)download NCBI ASN.1 biological sequence batches✨
• ds2pme(1)convert PubMed DocumentSummary XML to Pubmed-entry ASN.1 text✨

E

• eaddress(1)check edirect's notion of your e-mail address (DEPRECATED)✨
• eblast(1)perform a remote NCBI BLAST protein query (DEPRECATED)✨
• ecitmatch(1)look up a citation's PubMed ID (DEPRECATED)✨
• ecollect(1)list NCBI Entrez unique identifiers✨
• econtact(1)adjust contact information for an edirect pipeline (DEPRECATED)✨
• edict(1)HTTP server for EDirect local PubMed archive and search system✨
• edirect(1)access NCBI Entrez from the command line (DEPRECATED)✨
• edirutil(1)synthesize NCBI ENTREZ_DIRECT XML (DEPRECATED)✨
• efetch(1)retrieve results from an NCBI Entrez search✨
• efetch.ncbi(1)retrieve results from an NCBI Entrez search✨
• efilter(1)filter and/or sort NCBI Entrez search results✨
• einfo(1)look up general NCBI Entrez database information✨
• einfo.ncbi(1)look up general NCBI Entrez database information✨
• elink(1)look up related NCBI Entrez records✨
• enotify(1)send e-mail with NCBI Entrez search results (DEPRECATED)✨
• entrez-phrase-search(1)search NCBI Entrez for phrases (DEPRECATED)✨
• epost(1)upload a batch of NCBI Entrez record identifiers✨
• eproxy(1)load NCBI Entrez search aliases (DEPRECATED)✨
• esample(1)print a sample document for use with NCBI Entrez Direct✨
• esearch(1)search an NCBI Entrez database✨
• espell(1)spell-correct an NCBI Entrez query (DEPRECATED)✨
• esummary(1)retrieve results from an NCBI Entrez search✨
• exclude-uid-lists(1)compute the set difference of two numerical lists✨
• expand-current(1)expand a local NCBI PubMed archive✨

F

• fetch-pmc(1)fetch records from a local NCBI PubMed Central archive by UID✨
• fetch-pubmed(1)fetch records from a local NCBI PubMed archive by UID✨
• filter-columns(1)filter a tab-delimited table per custom criteria✨
• filter-genbank(1)filter structured files✨
• filter-record(1)filter structured files✨
• filter-stop-words(1)filter out unindexed NCBI Entrez words✨
• find-in-gene(1)list names of genes overlapping a range✨
• fsa2xml(1)XMLify✨
• ftp-cp(1)download files from an FTP server (DEPRECATED)✨
• ftp-ls(1)list directory entries on an FTP server (DEPRECATED)✨
• fuse-ranges(1)consolidate adjacent or overlapping integral ranges✨
• fuse-segments(1)consolidate adjacent or overlapping integral segments✨

G

• gbf2facds(1)convert NCBI GenBank flatfile coding sequences to FASTA✨
• gbf2fsa(1)convert NCBI GenBank flatfiles to FASTA✨
• gbf2info(1)convert NCBI GenBank flatfiles to GenBankInfo XML✨
• gbf2ref(1)XMLify✨
• gbf2tbl(1)transform a GenBank flatfile into an NCBI five-column feature table✨
• gbf2xml(1)XMLify✨
• gene2range(1)simplify NCBI Entrez gene document summaries for find-in-gene✨
• gff-sort(1)sort a General Feature Format version 3 file✨
• gff2xml(1)transform a General Feature Format version 3 file into XML✨
• gm2segs(1)present GeneMachine BLAST aligments in tabular form✨

H

• hgvs2spdi(1)transform genomic variation data from HGVS to SPDI format✨

I

• index-extras(1)populate and index local BioConcepts, GeneRifs, and theme data✨
• index-pubmed(1)maintain a local NCBI PubMed archive✨
• ini2xml(1)XMLify✨
• intersect-uid-lists(1)compute the intersection of two numerical lists✨

J

• join-into-groups-of(1)join input words into N-word groups✨
• json2xml(1)XMLify✨
• jsonl2xml(1)convert JSON to XML, one root object per input line.✨
• just-top-hits(1)truncate a tab-delimited file✨

N

• nquire(1)query NCBI Entrez Utilities, other parameter-based web services, or FTP✨

P

• pair-at-a-time(1)parse an input file into alphanumeric word pairs✨
• phrase-search(1)search an indexed local NCBI PubMed archive✨
• pm-clean(1)clean a local NCBI Entrez Direct archive✨
• pm-collect(1)collect records from a local NCBI PubMed archive✨
• pm-index(1)index a local NCBI PubMed archive✨
• pm-invert(1)prepare inverted indexes for a local NCBI PubMed archive✨
• pm-merge(1)merge inverted indexes for a local NCBI PubMed archive✨
• pm-prepare(1)prepare directories to hold a local NCBI Entrez Direct archive✨
• pm-promote(1)produce postings files for a local NCBI PubMed archive✨
• pm-refresh(1)refresh versioned NCBI PubMed records✨
• pm-setup(1)create directories to hold a local NCBI Entrez Direct archive✨
• pm-stash(1)expand a local NCBI PubMed archive into a trie✨
• pma2apa(1)convert PubmedArticle XML to APA-format citation✨
• pma2pme(1)convert PubmedArticle XML to Pubmed-entry ASN.1 text✨
• pmc2bioc(1)convert PubMed Central article XML to BioC collection XML✨
• pmc2info(1)convert PubMed Central article XML to PMCInfo XML for local archive✨
• print-columns(1)transform lines of a tab-delimited table✨
• print-missing-subranges(1)find gaps in a sorted list of numbers✨
• protein-neighbors(1)find similar protein accessions, via BLAST (DEPRECATED)✨

Q

• quote-grouped-elements(1)transform space-delimited table to quoted CSV✨

R

• rchive(1)work with a local archive of Entrez document summaries✨
• ref2pmid(1)match PubMed citations in Reference Index XML✨
• refseq-nm-cds(1)download NCBI RefSeq mRNAs and summarize coding regions✨
• reorder-columns(1)reorder columns of a tab-delimited file✨
• run-ncbi-converter(1)Run a converter from NCBI's FTP site✨

S

• scn2xml(1)XMLify✨
• skip-if-file-exists(1)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-by-length(1)sort text in increasing order of line length✨
• sort-table(1)sort a tab-delimited table✨
• sort-uniq-count(1)print line frequencies✨
• sort-uniq-count-rank(1)print line frequencies✨
• spdi2tbl(1)present NCBI SPDI-format SNP data in tabular form✨
• split-at-intron(1)summarize genomic insertions from blst2tkns output✨
• stream-pubmed(1)dump a local NCBI PubMed archive in compressed form✨
• systematic-mutations(1)print all single-nucleotide substitutions✨

T

• tbl2prod(1)pair modified mRNA and protein sequences for SNP data✨
• tbl2xml(1)XMLify✨
• theme-aliases(1)establish bash aliases for some phrase-search commands✨
• transmute(1)transform data, particularly within NCBI Entrez Direct✨

U

• uniq-table(1)print columns taking on multiple values✨

W

• word-at-a-time(1)parse an input file into alphanumeric words✨

X

• xfetch(1)fetch records from a local NCBI Entrez Direct archive by UID✨
• xfilter(1)filter local NCBI Entrez Direct archive search results✨
• xinfo(1)print aggregate information for a local NCBI Entrez Direct archive✨
• xlink(1)look up related local NCBI Entrez Direct archive search results✨
• xml2fsa(1)print FASTA sequence data for INSDSeq XML✨
• xml2tbl(1)transform INSDSeq XML into an NCBI five-column feature table✨
• xsearch(1)search an indexed local NCBI Entrez Direct archive✨
• xtract(1)NCBI Entrez Direct XML conversion and transformation tool✨
• xy-plot(1)produce and display a line graph✨

Y

• yaml2xml(1)XMLify✨