Last updated: 2026-01-05
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Knit directory: muse/
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Ignored: data/pbmc3k_export.mtx
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | b5e26c0 | Dave Tang | 2026-01-05 | Affiliations |
| html | f3e07e6 | Dave Tang | 2026-01-05 | Build site. |
| Rmd | 6eafc4d | Dave Tang | 2026-01-05 | Using the pubmedR package |
Following the brief demo.
install.packages("pubmedR")
install.packages("bibliometrix")Load library.
library(pubmedR)
packageVersion("pubmedR")[1] '0.0.3'Perform a query.
query <- "bibliometric*[Title/Abstract] AND english[LA] AND Journal Article[PT] AND 2000:2020[DP]"
res <- pmQueryTotalCount(query = query)
res$total_count[1] 3748| Affiliation [ad] | Full Investigator Name [fir] | Pagination [pg] |
| All Fields [all] | Grants and Funding [gr] | Personal Name as Subject [ps] |
| Article Identifier [aid] | Investigator [ir] | Pharmacological Action [pa] |
| Author [au] | ISBN [isbn] | Place of Publication [pl] |
| Author Identifier [auid] | Issue [ip] | PMCID and MID |
| Book [book] | Journal [ta] | PMID [pmid] |
| Comment Correction Type | Language [la] | Publication Date [dp] |
| Completion Date [dcom] | Last Author Name [lastau] | Publication Type [pt] |
| Conflict of Interest Statement [cois] | Location ID [lid] | Publisher [pubn] |
| Corporate Author [cn] | MeSH Date [mhda] | Secondary Source ID [si] |
| Create Date [crdt] | MeSH Major Topic [majr] | Subset [sb] |
| EC/RN Number [rn] | MeSH Subheadings [sh] | Supplementary Concept [nm] |
| Editor [ed] | MeSH Terms [mh] | Text Words [tw] |
| Entry Date [edat] | Modification Date [lr] | Title [ti] |
| Filter [filter] [sb] | NLM Unique ID [jid] | Title/Abstract [tiab] |
| First Author Name [1au] | Other Term [ot] | Transliterated Title [tt] |
| Full Author Name [fau] | Owner | Volume [vi] |
Search for some dude called Dave Tang.
query <- "Dave Tang[fau]"
res <- pmQueryTotalCount(query = query)
res$total_count
[1] 22
$query_translation
[1] "tang, dave[Author]"
$web_history
Web history object (QueryKey = 1, WebEnv = MCID_695b57a...)Download the collection of document metadata.
D <- pmApiRequest(query = query, limit = res$total_count, api_key = NULL)Documents 22 of 22 M <- pmApi2df(D)================================================================================Use some {bibliometrix} functions to get an overview of the bibliographic collection.
suppressPackageStartupMessages(library(bibliometrix))
M <- convert2df(D, dbsource = "pubmed", format = "api")
Converting your pubmed collection into a bibliographic dataframe
================================================================================
Done!results <- biblioAnalysis(M)
summary(results)
MAIN INFORMATION ABOUT DATA
Timespan 2008 : 2020
Sources (Journals, Books, etc) 14
Documents 21
Annual Growth Rate % 0
Document Average Age 12.5
Average citations per doc 0
Average citations per year per doc 0
References 1
DOCUMENT TYPES
case reports 2
comparative study 1
dataset 1
journal article 17
DOCUMENT CONTENTS
Keywords Plus (ID) 179
Author's Keywords (DE) 28
AUTHORS
Authors 194
Author Appearances 269
Authors of single-authored docs 0
AUTHORS COLLABORATION
Single-authored docs 0
Documents per Author 0.108
Co-Authors per Doc 12.8
International co-authorships % 0
Annual Scientific Production
Year Articles
2008 2
2009 3
2010 2
2011 1
2012 2
2014 1
2015 1
2016 4
2017 2
2018 1
2020 2
Annual Percentage Growth Rate 0
Most Productive Authors
Authors Articles Authors Articles Fractionalized
1 TANG D 17 TANG D 1.673
2 LASSMANN T 6 CARNINCI P 0.680
3 CARNINCI P 5 TANG DT 0.597
4 GRIMMOND SM 5 GRIMMOND SM 0.474
5 BLACKWELL JM 4 SAXENA A 0.444
6 CHIU HS 4 LASSMANN T 0.410
7 LITTLE MH 4 CHIU HS 0.331
8 TANG DT 4 LITTLE MH 0.331
9 ANDERSON D 3 BLACKWELL JM 0.308
10 GEORGAS KM 3 ANDERSON D 0.303
Top manuscripts per citations
Paper DOI TC TCperYear NTC
1 LASSMANN T, 2020, NPJ GENOM MED 10.1038/s41525-020-00161-w 0 0 NaN
2 ANDERSON D, 2020, SCI REP 10.1038/s41598-020-76157-4 0 0 NaN
3 BERTUZZI M, 2018, HUM MUTAT 10.1002/humu.23974 0 0 NaN
4 TANG D, 2017, SCI REP 10.1038/s41598-018-29279-9 0 0 NaN
5 ROTHACKER KM, 2017, INT J PEDIATR ENDOCRINOL 10.1186/s13633-018-0056-3 0 0 NaN
6 ROUDNICKY F, 2016, J PATHOL 10.1002/path.4892 0 0 NaN
7 HON CC, 2016, NATURE 10.1038/nature21374 0 0 NaN
8 ABRAHAM MB, 2016, INT J PEDIATR ENDOCRINOL 10.1186/s13633-016-0041-7 0 0 NaN
9 BAYNAM G, 2016, ORPHANET J RARE DIS 10.1186/s13023-016-0462-7 0 0 NaN
10 TANG D, 2015, SCI DATA 10.1038/sdata.2016.23 0 0 NaN
Corresponding Author's Countries
Country Articles Freq SCP MCP MCP_Ratio
1 NA 21 1 21 0 0
SCP: Single Country Publications
MCP: Multiple Country Publications
Total Citations per Country
Country Total Citations Average Article Citations
1 NA 0 0
Most Relevant Sources
Sources Articles
1 SCIENTIFIC REPORTS 3
2 BMC GENOMICS 2
3 DEVELOPMENTAL BIOLOGY 2
4 INTERNATIONAL JOURNAL OF PEDIATRIC ENDOCRINOLOGY 2
5 NATURE 2
6 PLOS ONE 2
7 BIOINFORMATICS (OXFORD ENGLAND) 1
8 DISEASE MARKERS 1
9 HUMAN MUTATION 1
10 NPJ GENOMIC MEDICINE 1
Most Relevant Keywords
Author Keywords (DE) Articles Keywords-Plus (ID) Articles
1 ANGIOGENESIS 1 ANIMALS 11
2 BLADDER CANCER 1 HUMANS 11
3 BLOOD TRANSCRIPTOMICS 1 MICE 8
4 CLINICAL BEST PRACTICE 1 GENOMICS 5
5 DESERT HEDGEHOG 1 GENE EXPRESSION PROFILING 4
6 DHH 1 GENOME-WIDE ASSOCIATION STUDY 4
7 DIAGNOSIS 1 HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING 4
8 DIAGNOSTIC ODYSSEY 1 POLYMORPHISM SINGLE NUCLEOTIDE 4
9 DISORDER OF SEX DEVELOPMENT 1 SEQUENCE ANALYSIS RNA 4
10 FAM111A GENE 1 AUSTRALIA 3Metadata.
names(results) [1] "Articles" "Authors" "AuthorsFrac" "FirstAuthors" "nAUperPaper"
[6] "Appearances" "nAuthors" "AuMultiAuthoredArt" "AuSingleAuthoredArt" "MostCitedPapers"
[11] "Years" "FirstAffiliation" "Affiliations" "Aff_frac" "CO"
[16] "Countries" "CountryCollaboration" "TotalCitation" "TCperYear" "Sources"
[21] "DE" "ID" "Documents" "IntColl" "nReferences"
[26] "DB" Affiliations.
results$Affiliations |>
as.data.frame() |>
dplyr::pull(AFF) |>
as.vector() |>
unique() |>
head(10) [1] "GENETIC SERVICES OF WESTERN AUSTRALIA, DEPARTMENT OF HEALTH, GOVERNMENT OF WESTERN AUSTRALIA, PERTH, WA, AUSTRALIA."
[2] "RIKEN CENTER FOR LIFE SCIENCE TECHNOLOGIES (DIVISION OF GENOMIC TECHNOLOGIES), 1-7-22 SUEHIRO-CHO, TSURUMI-KU, YOKOHAMA, 230-0045 JAPAN."
[3] "RIKEN OMICS SCIENCE CENTER (OSC), 1-7-22 SUEHIRO-CHO, TSURUMI-KU, YOKOHAMA 230-0045, JAPAN."
[4] "TELETHON KIDS INSTITUTE, UNIVERSITY OF WESTERN AUSTRALIA, PERTH, WA, AUSTRALIA."
[5] "TELETHON KIDS INSTITUTE, THE UNIVERSITY OF WESTERN AUSTRALIA, PERTH, WA, AUSTRALIA."
[6] "TELETHON KIDS INSTITUTE, THE UNIVERSITY OF WESTERN AUSTRALIA, SUBIACO, WESTERN AUSTRALIA 6008, AUSTRALIA."
[7] "TELETHON KIDS INSTITUTE, THE UNIVERSITY OF WESTERN AUSTRALIA, SUBIACO, WESTERN AUSTRALIA, 6008, AUSTRALIA."
[8] "AREA OF NEUROSCIENCE, SISSA, TRIESTE, ITALY."
[9] "INSTITUTE OF PHARMACEUTICAL SCIENCES, ETH ZURICH, ZURICH, SWITZERLAND."
[10] "1] OMICS SCIENCE CENTER, RIKEN YOKOHAMA INSTITUTE, 1-7-22 SUEHIRO-CHO TSURUMI-KU YOKOHAMA, KANAGAWA, 230-0045 JAPAN [2] RIKEN CENTER FOR LIFE SCIENCE TECHNOLOGIES, DIVISION OF GENOMIC TECHNOLOGIES, 1-7-22 SUEHIRO-CHO TSURUMI-KU YOKOHAMA, KANAGAWA, 230-0045 JAPAN."
sessionInfo()R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bibliometrix_5.0.1 pubmedR_0.0.3 lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[7] purrr_1.0.4 readr_2.1.5 tidyr_1.3.1 tibble_3.3.0 ggplot2_3.5.2 tidyverse_2.0.0
[13] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 viridisLite_0.4.2 farver_2.1.2 fastmap_1.2.0 lazyeval_0.2.2
[6] janeaustenr_1.0.0 promises_1.3.3 XML_3.99-0.18 digest_0.6.37 timechange_0.3.0
[11] mime_0.13 lifecycle_1.0.4 tokenizers_0.3.0 processx_3.8.6 magrittr_2.0.3
[16] compiler_4.5.0 rlang_1.1.6 sass_0.4.10 tools_4.5.0 igraph_2.1.4
[21] yaml_2.3.10 tidytext_0.4.2 data.table_1.17.4 knitr_1.50 htmlwidgets_1.6.4
[26] curl_6.4.0 plyr_1.8.9 RColorBrewer_1.1-3 ca_0.71.1 withr_3.0.2
[31] grid_4.5.0 git2r_0.36.2 xtable_1.8-4 scales_1.4.0 cli_3.6.5
[36] rmarkdown_2.29 generics_0.1.4 stringdist_0.9.15 rstudioapi_0.17.1 httr_1.4.7
[41] tzdb_0.5.0 visNetwork_2.1.2 readxl_1.4.5 cachem_1.1.0 rscopus_0.8.1
[46] parallel_4.5.0 cellranger_1.1.0 vctrs_0.6.5 Matrix_1.7-3 jsonlite_2.0.0
[51] callr_3.7.6 hms_1.1.3 ggrepel_0.9.6 plotly_4.11.0 jquerylib_0.1.4
[56] glue_1.8.0 ps_1.9.1 DT_0.33 stringi_1.8.7 gtable_0.3.6
[61] later_1.4.2 pillar_1.10.2 htmltools_0.5.8.1 bibliometrixData_0.3.0 R6_2.6.1
[66] rprojroot_2.0.4 evaluate_1.0.3 shiny_1.11.1 lattice_0.22-6 rentrez_1.2.4
[71] SnowballC_0.7.1 openxlsx_4.2.8 openalexR_2.0.1 httpuv_1.6.16 bslib_0.9.0
[76] Rcpp_1.0.14 zip_2.3.3 whisker_0.4.1 dimensionsR_0.0.3 xfun_0.52
[81] fs_1.6.6 getPass_0.2-4 pkgconfig_2.0.3