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Impact Analysis
363,951
Total Citations
30,918
Unique Citing Papers
2,334
Citing Fields
10,146
Citing Institutions
203
Linked Publications
35 canonical · 143 mentions · 25 papers
6,577
Papers Depending on Software
2124.3M
Package Downloads
118,756
Dependent Packages
26,708
External Users
Non-contributor participants
Publications
Total Citations363,951
Median Citations113
Portfolio FWCI72.79
Citation Trajectory
→1415
12
2065
13
2979
14
3743
15
5078
16
6944
17
10388
18
16345
19
26369
20
40359
21
45922
22
53218
23
65394
24
65021
25
15601
26
Repositories
Paper Connections203
Papers Depending on Software6,577
Package Downloads2124.3M
Dependent Packages118,756
Dependent Repos1,638,279
Adoption Signals
Issues from Users30,745
PRs from Users25,661
External Unique Users26,708
Publications
72.79FWCI (131 papers)
Percentile Distribution
Top 1% (120)Top 10% (7)No data (46)
Citation Distribution
0
23
1-5
13
6-20
16
21-50
14
51-100
20
101-500
30
500+
57
Top Papers
| Title | Cit. ▼ | FWCI | Pctl |
|---|---|---|---|
| Matplotlib: A 2D Graphics Environment | 37,869 | 30.17 | 100th |
| IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies | 26,786 | 74.72 | 100th |
| SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing | 26,638 | 93.32 | 100th |
| Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 | 23,068 | 720.21 | 100th |
| Array programming with NumPy | 20,849 | 1275.47 | 100th |
| Model-based Analysis of ChIP-Seq (MACS) | 19,576 | 53.39 | 100th |
| New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 | 18,743 | 197.07 | 100th |
| ModelFinder: fast model selection for accurate phylogenetic estimates | 17,996 | 1014.14 | 100th |
| Minimap2: pairwise alignment for nucleotide sequences | 16,048 | 367.05 | 100th |
| IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era | 15,730 | 511.83 | 100th |
Repositories
Top Repos by Paper Connections
| Repository | Citing | Mention | Total ▼ |
|---|---|---|---|
| brainglobe/brainglobe-atlasapi | 25 | 0 | 25 |
| iqtree/iqtree2 | 20 | 0 | 20 |
| ipinfo/python | 0 | 20 | 20 |
| sigmavirus24/github3 | 0 | 20 | 20 |
| bactopia/bactopia | 7 | 5 | 12 |
| matplotlib/matplotlib | 1 | 10 | 11 |
| scikit-learn/scikit-learn | 0 | 11 | 11 |
| numpy/numpy | 1 | 8 | 9 |
| scipy/scipy | 0 | 9 | 9 |
| docker/docker-py | 0 | 9 | 9 |
| pandas-dev/pandas | 2 | 6 | 8 |
| interactions-py/library | 0 | 8 | 8 |
| francescortiz/image | 0 | 7 | 7 |
| scikit-image/scikit-image | 1 | 5 | 6 |
| arviz-devs/arviz | 6 | 0 | 6 |
| saeyslab/nichenetr | 6 | 0 | 6 |
| sbmlteam/libsbml | 5 | 0 | 5 |
| pydata/xarray | 2 | 3 | 5 |
| deep-mi/fastsurfer | 5 | 0 | 5 |
| kubernetes-client/python | 0 | 5 | 5 |
Mention Sources
Softcite
685
CZI
871
SoftwareKG
485
435 software items confirmed by multiple sources
Publications
Citing Authors93,559
Citing Institutions10,174
Top Citing Institutions
Centre National de la Recherche Scientifique(FR)
719 citations
Chinese Academy of Sciences(CN)
505 citations
Harvard University(US)
485 citations
Uppsala University(SE)
470 citations
Science for Life Laboratory(SE)
446 citations
Karolinska Institutet(SE)
367 citations
Recent Citing Papers
- Good Scientific Practice in MEEG Research: Progress and Perspectives2021cites: A Reproducible MEG/EEG Group Study With the MNE Software: Recommendations, Quality Assessments, and Good Practices
- Hybridization and Polyploidy Shaped the Evolutionary History of a Complex of Cryptic Species in European Woodrushes ( <i>Luzula</i> sect. <i>Luzula</i> )2025cites: UFBoot2: Improving the Ultrafast Bootstrap Approximation
- Frequent Hybridisation Between Parapatric Lekking Bird‐of‐Paradise Species2025cites: IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
- Extensive folding variability between homologous chromosomes in mammalian cells2025cites: Model-based Analysis of ChIP-Seq (MACS)
- A scalable variational inference approach for increased mixed-model association power2025cites: PyTorch 2: Faster Machine Learning Through Dynamic Python Bytecode Transformation and Graph Compilation
Repositories
Software Used By
Harvard University(US)
16 papers
Stanford University(US)
13 papers
Australian National University(AU)
10 papers
Max Perutz Labs(AT)
10 papers
Heidelberg University(DE)
10 papers
Centre National de la Recherche Scientifique(FR)
10 papers
Medical University of Vienna(AT)
9 papers
University of California, San Francisco(US)
8 papers
University of Vienna(AT)
7 papers
University College London(GB)
7 papers
External User Breakdown
Issue Reporters25,679
Reviewers0
Triagers180
Supporters148
Publications
Citing Domains4
Citing Fields26
Citing Subfields225
Top Citing Fields
Biochemistry, Genetics and Molecular Biology11379
Medicine4118
Agricultural and Biological Sciences3877
Environmental Science3082
Computer Science1777
Immunology and Microbiology1395
Engineering1229
Neuroscience1008
Earth and Planetary Sciences765
Physics and Astronomy708
Top Citing Subfields
Molecular Biology8995
Genetics2568
Plant Science2251
Ecology2243
Artificial Intelligence983
Immunology963
Ecology, Evolution, Behavior and Systematics891
Biophysics783
Cell Biology761
Cancer Research760
Repositories
Software by Research Field
Biochemistry, Genetics and Molecular Biology
91
Computer Science
42
Medicine
29
Neuroscience
20
Decision Sciences
20
Environmental Science
15
Agricultural and Biological Sciences
15
Earth and Planetary Sciences
12
Engineering
8
Materials Science
8
Psychology
5
Immunology and Microbiology
3
Mathematics
3
Chemistry
3
Health Professions
2
Countries (33)
575
United States
219
Germany
134
United Kingdom
101
France
57
Canada
56
Austria
47
Denmark
45
Switzerland
41
Australia
36
Belgium
34
Norway
19
The Netherlands
18
Russia
12
Spain
10
Mexico
10
China
6
Singapore
5
Vietnam
5
Argentina
4
Finland
4
New Zealand
3
Türkiye
3
Sweden
3
Hungary
3
South Africa
3
Poland
2
Italy
2
Japan
1
Ireland
1
Portugal
1
South Korea
1
Bahamas
1
Czechia
343 institutions total, 343 with coordinates
Open Access Status
Gold OA
Green OA
Hybrid OA
Closed Access
Bronze OA
Unknown
Research Topics
Genomics and Phylogenetic Studies
37
Cell Image Analysis Techniques
22
Single-cell and spatial transcriptomics
21
Genetic diversity and population structure
17
Scientific Computing and Data Management
15
Functional Brain Connectivity Studies
12
Advanced MRI Techniques and Applications
10
Advanced Neuroimaging Techniques and Applications
10
Evolution and Paleontology Studies
9
Other
42
Publication Venues
Zenodo (CERN European Organization for Nuclear Research)
26
Nature Methods
10
Bioinformatics
10
Systematic Biology
8
Molecular Biology and Evolution
7
PLoS Computational Biology
6
The Journal of Open Source Software
5
Other
30