Last commit

Programming language use distribution from recent programs / articles


Usage: pubmedcodinglang [options] Files
    -c, --common
      [20180302] only common languages. What is a 'common' language ? well .. 
      it's subjective...
      Default: false
    -h, --help
      print help and exit
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
      print version and exit


See also in Biostars


Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew pubmedcodinglang

The java jar file will be installed in the dist directory.

Creation Date


Source code


Unit Tests




The project is licensed under the MIT license.


Should you cite pubmedcodinglang ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:


Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030


$ java -jar dist/pubmeddump.jar 'Bioinformatics 2017' | java -jar dist/pubmedcodinglang.jar

28464826	java	microTaboo: a general and practical solution to the k-disjoint problem.	2017	, running [java] 7 and hig
28453684	python	MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform.	2017	eloped in [python], using r 
28453672	python	Primerize-2D: automated primer design for RNA multidimensional chemical mapping.	2017	and-alone [python] package f
28449031	python	RNAblueprint: Flexible multiple target nucleic acid sequence design.	2017	ritten in [python] to demons
28444126	ruby	CImbinator: A web-based tool for drug synergy analysis in small- and large-scale datasets.	2017	ritten in [ruby] and r. it
28437135	python	D3GB: An Interactive Genome Browser for R, Python, and WordPress.	2017	ackage, a [python] module, a
28431529	python	HirBin: high-resolution identification of differentially abundant functions in metagenomes.	2017	nted as a [python] package a
28430977	java	Deep Mining Heterogeneous Networks of Biomedical Linked Data to Predict Novel Drug-Target Associations.	2017	eloped in [java] and it is
28415074	python	NaviCom: a web application to create interactive molecular network portraits using multi-level omics data.	2017	avicom, a [python] package a


cut -f2,4 output.txt  | sort | uniq -c |\
awk '{printf("%s\t%s\t%s\n",$3,$2,$1);}' | ./yxv2table -n 0 | grep -v '^null' | grep -v '^     ' | sed 's/^#/Year/' > table.txt && \
gnuplot script.gnuplot
set terminal png size 2000,1500;
set output "output.png"
set title "Bioinformatics/language"
set key invert reverse Left outside
set key autotitle columnheader
set yrange [0:]
set auto x
unset xtics
set xlabel "Year"
set ylabel "Count"
set xtics nomirror rotate by -45 scale 0
set style data histogram
set style histogram rowstacked
set style fill solid border -1
set boxwidth 0.75
N=`awk 'NR==1 {print NF}' table.txt`
plot 'table.txt' using 2:xtic(1), for [i=3:N] '' using i;


See also