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pubmed.mineR (version 1.0.19)
Text Mining of PubMed Abstracts
Description
Text mining of PubMed Abstracts (text and XML) from
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Install
install.packages('pubmed.mineR')
Monthly Downloads
726
Version
1.0.19
License
GPL-3
Maintainer
S. Ramachandran
Last Published
November 26th, 2021
Functions in pubmed.mineR (1.0.19)
Search functions
altnamesfun
To Get Alternative names of Genes
cleanabs
To clean the result of searchabsL
HGNCdata
R Data containing HGNC data.
contextSearch
For Context Search
genes_BWI
Function to obtain the Buzz Word Index of Genes from the abstracts.
get_DOIs
function for extracting Digital Object Identifier (DOIs) of papers
Give_Sentences_PMC
To fetch the sentence from the PMC full text article
getabsT-methods
To Get Abstracts
cluster_words
To Find the highest frequency of words within clusters
cos_sim_calc
To calculate the cosine similarity between terms.
Yearwise-methods
Yearwise
Year wise extraction of Abstracts
cleanabs-methods
Methods for Function
cleanabs
getabsT
To get Abstracts for a given term.
pmids_to_abstracts
To Find and match the PMIDs to the abstracts.
Yearwise
To Search abstracts Year wise
contextSearch-methods
Method for Context Search
common_words_new
R Data containing words which frequently in text
find_intro_conc_html
To find the introduction and conclusion from the abstracts.
currentabs_fn
To Retrive the Abstracts for year.
cos_sim_calc_boot
Cosine Similarity Calculation by Boot Strapping
previousabs_fn
To Retrieve the Abstracts from the large corpus for given years.
gene_atomization
To Extract Genes from the Abstracts
get_PMCIDS
To extract the PMC Ids of the abstracts.
removeabs
To remove abstracts for the query term.
uniprotfun
To get information about gene from the UniProt.Deprecated.
removeabs-methods
removeabs
To remove abstracts of a term from the data.
whichcluster
To fetch the cluster for words
get_original_term
To get the original terms from the corpus. deprecated
pubtator_function_JSON
function for text annotation using PubTator
input_for_find_intro_conc_html
fetch the abstracts using E-utilities.
pubtator_function
function for text annotation using PubTator
head_abbrev
To extract the abbreviated term.
get_original_term2
To get the original terms from the corpus.
additional_info
To extract sentences with nultiple keywords from Abstracts
alias_fn
To extract sentences containing Alias of the Human Genes from Pubmed abstracts.
get_PMCtable
To fetch the given PMC article tables. Deprecated
readabsnew
To read Abstracts
ready
To Initiate the Classes.
combineabs-methods
Abstracts
Method to Combine Abstracts
combineabs
To combine the abstracts
SentenceToken
To Tokenize the sentences
prevsymbol_fn
To extract the sentences containing Previous symbols of HGNC genes.
space_quasher
Removes extra spaces between words.
printabs
To prind the total number of abstracts in an S4 object of class Abstracts , its start and end
subabs-methods
Getting subabstracts
get_gene_sentences
To extract the sentences for genes from the corpus.
get_Sequences
To extract the Gene sequence from the NCBI.
co_occurrence_advance
Extracts multiple sentence with co-occurrence of two sets of terms)
readabs
To read Abstracts
pubtator_result_list_to_table
Function to Convert Pubtator result from list into Table
local_uniprotfun
To Get Information from Uniprot.
names_fn
To extract the sentences in asbtracts containing gene names from HGNC.
searchabsL-methods
Searching Abstracts
official_fn
To extract the sentences containing official gene symbol from abstracts.
new_xmlreadabs
To read the abstracts from the PubMed saved in XML format.
xmlgene_atomizations
Gene atomization of xml abstracts.Deprecated.
get_MedlinePlus
To Get MedLinePlus Summary
co_occurrence_fn
Extracts sentences with co-occurrence of two sets of terms
word_associations
Extracts the words associated (to the left and to the right) with a given word
searchabsL
To Search the abstracts of term(s) in a combination mode.
word_atomizations
Atomization of words
sendabs-methods
To send the Data into a File
sendabs
To send abstracts
subsetabs
To make subsets of large corpus.
xmlgene_atomizations_new
Gene atomization of xml abstracts.
getabs
To get Abstracts for a given term.
get_NMids
To extract NM ids from NCBI.
getabs-methods
getabs
To Get abstracts for a term
tdm_for_lsa
create Term Document Matrix for lsa analysis
searchabsT
To Search Abstracts
searchabsT-methods
searchabsT
Searching abstracts
subabs
To find sub-abstracts
subsetabs-methods
To make subset of Abstracts.
xmlreadabs
To read the abstracts from the PubMed saved in XML format.
xmlword_atomizations
Word atomizations of abstracts from xml format.
wordsclusterview
To view the words in cluster
wordscluster
To cluster the words
GeneToEntrez
Data containing Entrez Ids
Genewise
To Search the number of abstracts for Genes
Give_Sentences
To extract sentences from the Abstracts
Find_conclusion
To find the conclusion from the abstract(s).
HGNC2UniprotID
R Data containing HGNC2UniprotID data mapping.
Abstracts-class
Class
"Abstracts"
Abstract Class
HGNC-class
HGNC Class for package.
Genewise-methods
method to find the abstracts for the given gene.
BWI
To obtain the Buzz Word Index of terms from the Abstracts.