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"pubtator_function_JSON", "pubtator_result_list_to_table", "pubtator3_function", "readabs", "readabsnew", "ready", "removeabs", "searchabsL", "searchabsT", "sendabs", "SentenceToken", "space_quasher", "subabs", "subsetabs", "tdm_for_lsa", "uniprotfun", "whichcluster", "word_associations", "word_atomizations", "wordscluster", "wordsclusterview", "xmlgene_atomizations", "xmlgene_atomizations_new", "xmlreadabs", "xmlword_atomizations", "Yearwise" ], "_datasets": [ { "name": "common_words_new", "title": "R Data containing words which frequently in text", "object": "common_words_new", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "GeneToEntrez", "title": "Data containing Entrez Ids", "object": "GeneToEntrez", "class": [ "data.frame" ], "fields": [ "V1", "V2" ], "rows": 21116, "table": true, "tojson": true }, { "name": "HGNC2UniprotID", "title": "R Data containing HGNC2UniprotID data mapping.", "object": "HGNC2UniprotID", "class": [ "data.frame" ], "fields": [ "From", "To" ], "rows": 67042, "table": true, "tojson": true }, { "name": "HGNCdata", "title": "R Data containing HGNC data.", "object": "HGNCdata", "class": [ "data.table", "data.frame" ], "fields": [ "hgnc_id", "symbol", "name" ], "rows": 42368, "table": true, "tojson": true } ], "_help": [ { "page": "Abstracts-class", "title": "Class '\"Abstracts\"' Abstract Class", "topics": [ "Abstracts-class" ] }, { "page": "additional_info", "title": "To extract sentences with nultiple keywords from Abstracts", "topics": [ "additional_info" ] }, { "page": "alias_fn", "title": "To extract sentences containing Alias of the Human Genes from Pubmed abstracts.", "topics": [ "alias_fn" ] }, { "page": "altnamesfun", "title": "To Get Alternative names of Genes", "topics": [ "altnamesfun" ] }, { "page": "BWI", "title": "To obtain the Buzz Word Index of terms from the Abstracts.", "topics": [ "BWI" ] }, { "page": "cleanabs", "title": "To clean the result of searchabsL", "topics": [ "cleanabs" ] }, { "page": "cleanabs-methods", "title": "Methods for Function 'cleanabs'", "topics": [ "cleanabs,Abstracts-method", "cleanabs-methods" ] }, { "page": "cluster_words", "title": "To Find the highest frequency of words within clusters", "topics": [ "cluster_words" ] }, { "page": "co_occurrence_advance", "title": "Extracts multiple sentence with co-occurrence of two sets of terms)", "topics": [ "co_occurrence_advance" ] }, { "page": "co_occurrence_fn", "title": "Extracts sentences with co-occurrence of two sets of terms", "topics": [ "co_occurrence_fn" ] }, { "page": "combineabs", "title": "To combine the abstracts", "topics": [ "combineabs" ] }, { "page": "combineabs-methods", "title": "'Abstracts' Method to Combine Abstracts", "topics": [ "combineabs,Abstracts-method", "combineabs-methods" ] }, { "page": "common_words_new", "title": "R Data containing words which frequently in text", "topics": [ "common_words_new" ] }, { "page": "contextSearch", "title": "For Context Search", "topics": [ "contextSearch" ] }, { "page": "contextSearch-methods", "title": "Method for Context Search", "topics": [ "contextSearch,Abstracts-method", "contextSearch-methods" ] }, { "page": "cos_sim_calc", "title": "To calculate the cosine similarity between terms.", "topics": [ "cos_sim_calc" ] }, { "page": "cos_sim_calc_boot", "title": "Cosine Similarity Calculation by Boot Strapping", "topics": [ "cos_sim_calc_boot" ] }, { "page": "currentabs_fn", "title": "To Retrive the Abstracts for year.", "topics": [ "currentabs_fn" ] }, { "page": "Find_conclusion", "title": "To find the conclusion from the abstract(s).", "topics": [ "Find_conclusion" ] }, { "page": "find_intro_conc_html", "title": "To find the introduction and conclusion from the abstracts.", "topics": [ "find_intro_conc_html" ] }, { "page": "gene_atomization", "title": "To Extract Genes from the Abstracts", "topics": [ "gene_atomization" ] }, { "page": "genes_BWI", "title": "Function to obtain the Buzz Word Index of Genes from the abstracts.", "topics": [ "genes_BWI" ] }, { "page": "GeneToEntrez", "title": "Data containing Entrez Ids", "topics": [ "GeneToEntrez" ] }, { "page": "Genewise", "title": "To Search the number of abstracts for Genes", "topics": [ "Genewise" ] }, { "page": "Genewise-methods", "title": "method to find the abstracts for the given gene.", "topics": [ "Genewise,Abstracts-method", "Genewise-methods" ] }, { "page": "get_DOIs", "title": "function for extracting Digital Object Identifier (DOIs) of papers", "topics": [ "get_DOIs" ] }, { "page": "get_gene_sentences", "title": "To extract the sentences for genes from the corpus.", "topics": [ "get_gene_sentences" ] }, { "page": "get_MedlinePlus", "title": "To Get MedLinePlus Summary", "topics": [ "get_MedlinePlus" ] }, { "page": "get_NMids", "title": "To extract NM ids from NCBI.", "topics": [ "get_NMids" ] }, { "page": "get_original_term", "title": "To get the original terms from the corpus. deprecated", "topics": [ "get_original_term" ] }, { "page": "get_original_term2", "title": "To get the original terms from the corpus.", "topics": [ "get_original_term2" ] }, { "page": "get_PMCIDS", "title": "To extract the PMC Ids of the abstracts.", "topics": [ "get_PMCIDS" ] }, { "page": "get_PMCtable", "title": "To fetch the given PMC article tables. Deprecated", "topics": [ "get_PMCtable" ] }, { "page": "get_Sequences", "title": "To extract the Gene sequence from the NCBI.", "topics": [ "get_Sequences" ] }, { "page": "getabs", "title": "To get Abstracts for a given term.", "topics": [ "getabs" ] }, { "page": "getabs-methods", "title": "'getabs' To Get abstracts for a term", "topics": [ "getabs,Abstracts-method", "getabs-methods" ] }, { "page": "getabsT", "title": "To get Abstracts for a given term.", "topics": [ "getabsT" ] }, { "page": "getabsT-methods", "title": "To Get Abstracts", "topics": [ "getabsT,Abstracts-method", "getabsT-methods" ] }, { "page": "Give_Sentences", "title": "To extract sentences from the Abstracts", "topics": [ "Give_Sentences" ] }, { "page": "Give_Sentences_PMC", "title": "To fetch the sentence from the PMC full text article", "topics": [ "Give_Sentences_PMC" ] }, { "page": "head_abbrev", "title": "To extract the abbreviated term.", "topics": [ "head_abbrev" ] }, { "page": "HGNC-class", "title": "HGNC Class for package.", "topics": [ "HGNC-class" ] }, { "page": "HGNC2UniprotID", "title": "R Data containing HGNC2UniprotID data mapping.", "topics": [ "HGNC2UniprotID" ] }, { "page": "HGNCdata", "title": "R Data containing HGNC data.", "topics": [ "HGNCdata" ] }, { "page": "input_for_find_intro_conc_html", "title": "fetch the abstracts using E-utilities.", "topics": [ "input_for_find_intro_conc_html" ] }, { "page": "local_uniprotfun", "title": "To Get Information from Uniprot.", "topics": [ "local_uniprotfun" ] }, { "page": "names_fn", "title": "To extract the sentences in asbtracts containing gene names from HGNC.", "topics": [ "names_fn" ] }, { "page": "new_xmlreadabs", "title": "To read the abstracts from the PubMed saved in XML format.", "topics": [ "new_xmlreadabs" ] }, { "page": "official_fn", "title": "To extract the sentences containing official gene symbol from abstracts.", "topics": [ "official_fn" ] }, { "page": "pmids_to_abstracts", "title": "To Find and match the PMIDs to the abstracts.", "topics": [ "pmids_to_abstracts" ] }, { "page": "previousabs_fn", "title": "To Retrieve the Abstracts from the large corpus for given years.", "topics": [ "previousabs_fn" ] }, { "page": "prevsymbol_fn", "title": "To extract the sentences containing Previous symbols of HGNC genes.", "topics": [ "prevsymbol_fn" ] }, { "page": "printabs", "title": "To prind the total number of abstracts in an S4 object of class Abstracts , its start and end", "topics": [ "printabs" ] }, { "page": "pubtator_function", "title": "function for text annotation using PubTator.Deprecated.", "topics": [ "pubtator_function" ] }, { "page": "pubtator_function_JSON", "title": "function for text annotation using PubTator", "topics": [ "pubtator_function_JSON" ] }, { "page": "pubtator_result_list_to_table", "title": "Function to Convert Pubtator result from list into Table", "topics": [ "pubtator_result_list_to_table" ] }, { "page": "pubtator3_function", "title": "function for text annotation using PubTator", "topics": [ "pubtator3_function" ] }, { "page": "readabs", "title": "To read Abstracts", "topics": [ "readabs" ] }, { "page": "readabsnew", "title": "To read Abstracts", "topics": [ "readabsnew" ] }, { "page": "ready", "title": "To Initiate the Classes.", "topics": [ "ready" ] }, { "page": "removeabs", "title": "To remove abstracts for the query term.", "topics": [ "removeabs" ] }, { "page": "removeabs-methods", "title": "'removeabs' To remove abstracts of a term from the data.", "topics": [ "removeabs,Abstracts-method", "removeabs-methods" ] }, { "page": "searchabsL", "title": "To Search the abstracts of term(s) in a combination mode.", "topics": [ "searchabsL" ] }, { "page": "searchabsL-methods", "title": "Searching Abstracts", "topics": [ "searchabsL,Abstracts-method", "searchabsL-methods" ] }, { "page": "searchabsT", "title": "To Search Abstracts", "topics": [ "searchabsT" ] }, { "page": "searchabsT-methods", "title": "'searchabsT' Searching abstracts", "topics": [ "searchabsT,Abstracts-method", "searchabsT-methods" ] }, { "page": "sendabs", "title": "To send abstracts", "topics": [ "sendabs" ] }, { "page": "sendabs-methods", "title": "To send the Data into a File", "topics": [ "sendabs,Abstracts-method", "sendabs-methods" ] }, { "page": "SentenceToken", "title": "To Tokenize the sentences", "topics": [ "SentenceToken" ] }, { "page": "space_quasher", "title": "Removes extra spaces between words.", "topics": [ "space_quasher" ] }, { "page": "subabs", "title": "To find sub-abstracts", "topics": [ "subabs" ] }, { "page": "subabs-methods", "title": "Getting subabstracts", "topics": [ "subabs,Abstracts-method", "subabs-methods" ] }, { "page": "subsetabs", "title": "To make subsets of large corpus.", "topics": [ "subsetabs" ] }, { "page": "subsetabs-methods", "title": "To make subset of Abstracts.", "topics": [ "subsetabs,Abstracts-method", "subsetabs-methods" ] }, { "page": "tdm_for_lsa", "title": "create Term Document Matrix for lsa analysis", "topics": [ "tdm_for_lsa" ] }, { "page": "uniprotfun", "title": "To get information about gene from the UniProt.Deprecated.", "topics": [ "uniprotfun" ] }, { "page": "whichcluster", "title": "To fetch the cluster for words", "topics": [ "whichcluster" ] }, { "page": "word_associations", "title": "Extracts the words associated (to the left and to the right) with a given word", "topics": [ "word_associations" ] }, { "page": "word_atomizations", "title": "Atomization of words", "topics": [ "word_atomizations" ] }, { "page": "wordscluster", "title": "To cluster the words", "topics": [ "wordscluster" ] }, { "page": "wordsclusterview", "title": "To view the words in cluster", "topics": [ "wordsclusterview" ] }, { "page": "xmlgene_atomizations", "title": "Gene atomization of xml abstracts.Deprecated.", "topics": [ "xmlgene_atomizations" ] }, { "page": "xmlgene_atomizations_new", "title": "Gene atomization of xml abstracts.", "topics": [ "xmlgene_atomizations_new" ] }, { "page": "xmlreadabs", "title": "To read the abstracts from the PubMed saved in XML format.", "topics": [ "xmlreadabs" ] }, { "page": "xmlword_atomizations", "title": "Word atomizations of abstracts from xml format.", "topics": [ "xmlword_atomizations" ] }, { "page": "Yearwise", "title": "To Search abstracts Year wise", "topics": [ "Yearwise" ] }, { "page": "Yearwise-methods", "title": "'Yearwise' Year wise extraction of Abstracts", "topics": [ "Yearwise,Abstracts-method", "Yearwise-methods" ] } ], "_rundeps": [ "bitops", "boot", "R2HTML", "RCurl", "RJSONIO", "XML" ], "_score": 2.7558748556724915, "_indexed": true, "_nocasepkg": "pubmed.miner", "_universes": [ "ramuigibnew" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.21", "date": "2026-05-26T06:01:25.000Z", "distro": "noble", "commit": "fda200ef9d555102b83fcdcb260443f4549b8743", "fileid": "f931432e3644edae231a4e065d89f6e73c2f20a238e31c3343dba9e5e4664f58", "status": "success", "check": "OK", "buildurl": 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