Man pages for pubmed.mineR
Text Mining of PubMed Abstracts

Abstracts-classClass '"Abstracts"' Absract Class
alias_fnTo Find Alias of the Genes.
altnamesfunTo Get Alternative names of Genes
BWITo Get the Buzz Word Index of terms form the Abstracts.
cleanabsTo clean the result of searchabsL
cleanabs-methodsMethods for Function 'cleanabs'
cluster_wordsTo Find the highest frequency of words within clusters
combineabsTo combine the abstracts
combineabs-methods'Abstracts' Method to Combine Abstracts
common_words_newR Data containing words which frequently in text
contextSearchFor Context Search
contextSearch-methodsMethod for Context Search
cos_sim_calcTo calculate the cosine similarity between terms.
cos_sim_calc_bootCosine Similarity Calculation by Boot Strapping
currentabs_fnTo Retrive the Abstracts for year.
Find_conclusionTo find the conclusion from the abstract(s).
find_intro_conc_htmlTo find the introduction and conclusion from the abstracts.
gene_atomizationTo Extract Genes from the Abstracts
genes_BWIFunction to get the Buzz Word Index of Genes from the...
GeneToEntrezData containing Entrez Ids
GenewiseTo Search the number of abstracts for Genes
Genewise-methodsmethod to find the abstracts for the given gene.
getabsTo get Abstracts for a given term.
getabs-methods'getabs' To Get abstracts for a term
getabsTTo get Abstracts for a given term.
getabsT-methodsTo Get Abstracts
get_gene_sentencesTo extract the sentences for genes from the corpus.
get_MedlinePlusTo Get MedLinePlus Summary
get_NMidsTo extract NM ids from NCBI.
get_original_termTo get the original terms from the corpus.
get_original_term2To get the original terms from the corpus.
get_PMCIDSTo extract the PMC Ids of the abstracts.
get_PMCtableTo fetch the given PMC article.
get_SequencesTo extract the Gene sequence from the NCBI.
Give_SentencesTo extract sentences from the Abstracts
Give_Sentences_PMCTo fetch the sentence from the PMC full text article
head_abbrevTo extract the abbreviated term.
HGNC2UniprotIDR Data containing HGNC2UniprotID data mapping.
HGNC-classHGNC Class for package.
HGNCdataR Data containing HGNC data.
input_for_find_intro_conc_htmlfetch the abstracts using E-utilities.
local_uniprotfunTo Get Information from Uniprot.
names_fnTo extract the gene names from HGNC.
official_fnTo extract the official gene symbol.
pmids_to_abstractsTo Find and match the PMIDs to the abstracts.
previousabs_fnTo Retrive the Abstracts from the large corpus for given...
prevsymbol_fnTo Find Previous symbols of genes.
printabsTo prind the total number of abstracts in an S4 object of...
pubtator_functionfunction for text annotation uisng online PubTator
pubtator_result_list_to_tableFunction to Convert Pubtator result from list into Table
readabsTo read Abstracts
readyTo Initiate the Classes.
removeabsTo remove abstracts for the query term.
removeabs-methods'removeabs' To remove abstracts of a term from the data.
searchabsLTo Search the abstracts of term(s) in a combination mode.
searchabsL-methodsSearching Abstracts
searchabsTTo Search Abstracts
searchabsT-methods'searchabsT' Searching abstracts
sendabsTo send abstracts
sendabs-methodsTo send the Data into a File
SentenceTokenTo Tokenize the sentences
subabsTo find sub-abstracts
subabs-methodsGetting subabstracts
subsetabsTo make subsets of large corpus.
subsetabs-methodsTo make subset of Abstracts.
tdm_for_lsacreate Term Document Matrix for lsa analysis
uniprotfunTo get information about gene from the UniProt.
whichclusterTo fetch the cluster for words
word_atomizationsAtomization of words
wordsclusterTo cluster the words
wordsclusterviewTo view the words in cluster
xmlgene_atomizationsGene atomization of xml abstracts.
xmlreadabsTo read the abstracts from the PubMed saved in XML format.
xmlword_atomizationsWord atomizations of abstracts from xml format.
YearwiseTo Search abstracts Year wise
Yearwise-methods'Yearwise' Year wise extraction of Abstracts
pubmed.mineR documentation built on Sept. 12, 2017, 9:02 a.m.