Man pages for pubmed.mineR
Text Mining of PubMed Abstracts

Abstracts-classClass '"Abstracts"' Abstract Class
alias_fnTo extract sentences containing Alias of the Human Genes from...
altnamesfunTo Get Alternative names of Genes
BWITo obtain the Buzz Word Index of terms from 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
co_occurrence_fnExtracts sentences with co-occurrence of two sets of terms
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 obtain 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. deprecated
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 tables. Deprecated
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 sentences in asbtracts containing gene names...
official_fnTo extract the sentences containing official gene symbol from...
pmids_to_abstractsTo Find and match the PMIDs to the abstracts.
previousabs_fnTo Retrieve the Abstracts from the large corpus for given...
prevsymbol_fnTo extract the sentences containing Previous symbols of HGNC...
printabsTo prind the total number of abstracts in an S4 object of...
pubtator_functionfunction for text annotation using PubTator
pubtator_result_list_to_tableFunction to Convert Pubtator result from list into Table
readabsTo read Abstracts
readabsnewTo 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
space_quasherRemoves extra spaces between words.
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 Aug. 17, 2018, 9:05 a.m.