software,num_papers_2023,num_papers_2022,num_papers_2021,num_papers_2020,num_papers_2019,num_papers_2018,num_papers_2017,num_papers_2016,num_papers_2013
3D Slicer,509,962,758,470,334,189,137,96,40
alevin-fry,9,5,5,0,0,0,0,0,0
Apache Arrow,8,7,4,3,3,0,0,0,0
Apollo,108,234,225,148,138,69,44,48,26
ArviZ,25,20,17,8,0,0,0,0,0
bcbio-nextgen,13,32,34,23,35,11,2,3,1
bedtools,2057,3227,3225,2738,3090,1067,851,663,212
BigDataViewer,21,33,28,21,25,7,4,4,0
Binder,20,35,44,46,54,7,6,7,1
Bio-Formats,30,50,52,50,32,18,13,12,2
Bioconda,90,152,177,172,162,33,9,3,0
Bioconductor,4880,8717,8949,6927,7071,2909,2670,2253,1233
Bokeh,22,36,32,36,29,7,3,1,1
BrainGlobe Atlas API,4,8,5,1,0,0,0,0,0
brainreg,6,13,10,3,0,1,0,0,0
brainrender,27,23,22,5,1,0,0,0,0
BWA,2390,5230,4959,4125,4347,2053,1614,1399,574
Cardinal,19,27,20,17,11,6,4,5,0
Catalyst,25,57,53,25,26,20,14,20,9
CCTBX,11,15,20,13,26,10,11,11,7
cellfinder,11,15,15,8,11,6,8,1,5
cgap-portal,0,0,0,0,0,0,0,0,0
ChimeraX,2692,4757,4121,3148,2322,1069,924,756,373
CLIJ,7,25,11,6,2,0,0,0,0
cogent3,1,0,2,0,0,0,0,0,0
conda-forge,3,9,7,3,5,1,1,0,0
conda-smithy,0,0,0,0,0,0,0,0,0
Cornerstone,2,5,1,3,2,1,0,2,0
CuPy,24,22,16,7,3,0,0,0,0
cuttlefish,11,12,8,1,1,0,0,0,0
CWL,7,16,23,14,35,5,5,4,0
Cytoscape,4706,11452,9624,6683,5057,2631,2178,1600,729
D4TOOLS,0,0,0,0,0,0,0,0,0
Dash,62,144,132,83,44,24,27,23,10
Dask,37,49,48,34,22,2,3,0,0
Datoviz,0,0,1,0,0,0,0,0,0
DeepLabCut,468,527,407,234,90,2,0,0,0
demuxlet,39,56,56,35,28,6,1,0,0
DESeq2,7708,13494,11275,7854,6642,2615,1874,1161,239
Deviser,0,0,0,1,0,0,0,0,0
DifferentialEquations,33,45,35,23,11,2,0,0,0
DIPY,67,95,97,63,82,16,17,9,1
dMRIPrep,2,2,1,1,0,0,0,0,0
doFuture,0,0,1,0,1,0,0,0,0
dynamo,128,170,154,113,95,57,34,34,17
dynast,1,1,0,0,0,0,0,0,0
dynverse,19,24,21,13,11,0,0,0,0
eddymotion,0,0,0,0,0,0,0,0,0
edgeR,2934,5589,5472,4288,3911,1540,1361,971,226
elastix,103,181,186,119,136,74,52,45,19
ETE Toolkit,24,33,41,23,26,16,9,4,0
FastSurfer,14,42,22,7,0,0,0,0,0
fMRIPrep,312,406,344,176,74,8,2,0,0
freemuxlet,9,14,8,6,2,0,0,0,0
FreeSurfer,1493,2682,2635,2152,2059,829,654,555,257
Funsor,0,0,0,0,0,0,0,0,0
future,18,32,16,6,7,10,3,4,2
Galata,0,0,0,0,0,0,0,0,0
galaxy,50,99,58,52,45,26,25,10,1
Galaxy,860,1702,1673,1288,1441,578,521,452,247
GATK,1888,3765,3583,2937,3569,1407,1139,1008,282
genome-sampler,0,4,1,1,0,0,0,0,0
GGD,3,3,3,3,2,0,0,0,1
Giotto,87,114,60,14,3,2,0,0,0
Glimma,57,82,88,61,43,9,8,0,0
granite,1,5,2,3,2,3,1,0,2
GraphBin,7,12,12,1,0,0,0,0,0
GSVA,1339,2904,1372,533,257,51,35,26,6
Hifiasm,235,250,93,6,0,0,0,0,0
HiGlass,54,117,94,45,39,10,2,0,0
Holoviz,3,6,10,5,0,0,0,0,0
HTSJDK,2,6,9,5,9,2,1,2,0
ICY,110,177,206,175,181,62,60,52,14
igraph,748,1332,1248,813,840,318,273,197,64
ilastik,325,456,388,253,211,60,38,26,6
ImageJ/Fiji,27474,56343,51666,42311,36124,21203,19022,15431,7540
ImgLib2,3,14,18,14,16,2,2,2,1
Integrative Modeling Platform,4,10,18,9,17,2,5,2,0
IPython,50,87,103,85,184,57,49,68,16
IQ-TREE,2295,3761,3296,1894,1231,372,138,64,2
ITK-SNAP,351,671,565,316,219,104,77,44,25
JBrowse,105,205,184,178,251,90,76,78,19
JupyterHub,10,15,14,13,10,1,1,0,0
JupyterLab,60,94,67,45,9,3,0,0,0
kallisto,552,902,944,758,697,190,92,40,0
KNIME,106,271,233,225,190,102,82,72,28
libSBML,10,14,22,17,24,13,9,8,12
limma,3839,8255,6588,4354,3527,1561,1375,1092,642
MACS,1277,2028,1970,1541,1656,567,472,395,184
mamba,10,20,8,7,7,1,2,1,2
Matplotlib,1661,2682,2293,1416,1174,329,242,180,64
MDAnalysis,228,258,221,139,78,30,31,22,9
memento,16,17,13,9,7,5,2,9,1
MetaCoAG,3,4,1,0,0,0,0,0,0
MicrobiomeDB.org,0,0,0,0,0,0,0,0,0
MicroManager,270,420,435,346,489,134,113,94,35
Minimap2,1379,1868,1675,1025,610,62,16,4,2
mixtools,37,71,105,72,101,33,27,29,9
MNE-BIDS-pipeline,2,0,1,0,0,0,0,0,0
MNE-Python,4049,9458,8264,7796,7710,5363,5064,4702,2720
MoBIE,6,7,5,1,0,0,1,0,0
ModelingToolkit,8,4,3,0,0,0,0,0,0
MONAILabel,0,0,0,0,0,0,0,0,0
Monocle,739,1167,877,557,463,96,34,27,0
MRIQC,82,101,90,53,55,8,2,2,0
MSstats,70,115,113,100,77,25,22,17,1
napari,100,82,45,13,1,0,0,0,0
NetworkX,343,566,505,337,327,86,61,53,32
Nextflow,341,427,340,186,137,19,13,3,0
nf-core,235,213,135,59,8,0,0,0,0
NGFF,2,1,1,0,0,0,0,0,0
Nibabel,38,70,59,41,30,8,2,3,2
Nilearn,125,162,153,121,87,11,11,5,0
NiReports,0,0,0,0,0,0,0,0,0
NumPy,1820,3073,2605,1500,1265,344,249,207,83
NumPyro,13,16,9,0,0,0,0,0,0
ODK,46,138,112,74,49,38,29,14,3
OHDSI,3,24,28,14,7,4,2,1,0
OHIF,2,4,0,1,0,0,0,0,0
OMOP Common Data Model,2,2,4,2,0,0,0,0,0
Open DBDP,0,0,0,0,0,0,0,0,0
Open Microscopy Environment,4,12,4,15,11,4,4,5,4
OpenBLAS,11,12,10,10,14,5,5,3,0
OpenCRAVAT,9,16,14,5,3,0,0,0,0
OpenFE,0,0,0,0,0,0,0,0,0
OpenFF,8,15,3,7,0,0,0,0,0
OpenFold,31,14,0,0,0,0,0,0,0
OpenMM,377,496,390,263,188,64,34,16,3
OpenMS,49,91,98,86,88,34,28,19,14
OpenPolscope,1,2,5,3,3,1,2,0,0
OpenPose,106,251,146,89,33,4,0,0,0
OpenRefine,16,35,16,14,14,12,10,4,2
OpenSim,144,251,190,123,123,61,40,32,10
OpenSPIM,7,18,18,27,28,9,9,7,2
Orange Data Mining,10,13,12,6,1,1,0,1,0
pandas,1321,2125,1763,987,693,150,91,54,4
Parsl,0,8,9,3,4,0,0,0,0
Percolator,249,384,349,302,244,91,85,69,14
PhasorPy,0,0,0,0,0,0,0,0,0
phy,90,141,119,68,47,27,20,30,13
pip,41,75,63,49,71,19,11,10,3
progressr,0,0,0,0,0,0,0,0,0
Protege,40,109,92,57,58,57,53,55,47
PsychoJS,12,17,7,4,0,0,0,0,0
PsychoPy,356,645,525,450,411,133,116,86,17
pufferfish,3,8,4,5,4,1,0,0,0
PyData Sphinx,0,0,0,0,0,0,0,0,0
Pygfx,0,0,0,0,0,0,0,0,0
PyMC,79,118,168,114,101,27,12,10,7
Pyro,31,44,32,17,19,4,5,4,6
qFit,13,13,14,7,20,8,2,1,1
QIIME2,2238,5357,4301,3428,3018,1735,1339,953,220
QUAST,736,1265,1206,957,835,352,229,129,7
quetz,0,0,0,0,0,0,0,0,0
QuPath,791,1029,713,302,130,29,4,1,0
Read the Docs,7,10,13,7,6,1,1,1,0
ROBOT,21,50,45,33,14,8,6,10,2
Rocker,6,12,10,9,16,2,2,5,0
rocker,6,12,10,9,16,2,2,5,0
salmon,597,877,804,551,397,94,44,16,0
Scanpy,940,974,727,423,204,8,0,0,0
scikit-image,291,420,362,221,197,35,30,23,1
scikit-learn,3883,6440,5422,3370,2384,635,347,204,18
SciML,11,8,11,2,2,0,0,0,0
SciPy,1620,2443,2113,1357,1036,271,233,152,66
scvi-tools,71,78,29,0,0,0,0,0,0
seqr,21,24,18,12,8,6,2,0,1
Seurat,3450,4806,3427,1989,994,140,45,17,2
Simbody,4,12,10,9,12,2,1,5,0
Slicer,509,962,758,470,334,189,137,96,40
SlicerIGT,0,5,5,4,0,1,0,0,0
SMPLify-X,1,3,0,0,0,0,0,0,0
SPAdes,1239,2631,2757,2306,2276,1049,827,597,15
Spateo,9,0,0,0,0,0,0,0,0
Spyder,54,123,85,48,27,4,4,2,1
Stan,674,1106,1220,714,612,197,139,73,5
SymPy,16,51,38,34,42,12,6,6,3
Tibanna,0,1,5,1,1,0,0,0,0
tolerance,0,5,2,1,0,0,0,0,1
UCSC Xena,341,705,723,564,556,208,165,130,90
upset,90,122,137,104,104,24,18,3,1
VisPy,3,3,1,1,3,1,1,1,1
VTK,60,97,83,63,47,31,37,28,21
WESTPA,13,11,15,7,4,2,1,1,0
Xarray,20,28,30,14,11,2,2,0,0
Zarr,18,12,15,4,1,0,0,0,0