Citation-File Projects (2026-05-08)

Public

Every GitHub repository known to publish a CITATION.cff or CITATION.bib file as of 2026-05-08. The Citation File Format (CFF) is a community standard that lets software authors declare exactly how they want their work to be cited — author lists, DOIs, version, release date, related preferred citations. A repository that ships a CITATION file is making an explicit, machine-readable statement: this is research software, and here is how to credit it. This portfolio is a snapshot of that population: roughly 47,000 repositories spanning the long tail of scientific computing — niche domain tools, dissertation code, lab software, individual researcher libraries, and the well-known frameworks alongside them. Together they offer a view of research software practice that does not depend on package-registry presence, citation in a journal, or membership in a foundation: it captures everyone who took the time to say "please cite me this way." Built from the latest citation-file index, normalized to one canonical GitHub URL per repository.

Created 5/12/2026 - Last updated 9/9/2026

47.3K

Projects

24.7M commits

369.6K

Recognition

316.6K citing papers · 7.3K canonical works

2.0M

Reach

245.5K external users · 3058.9M downloads

35.9K

Repositories at risk

79% of 45.7K evaluated · 9.8K healthy · 1.6K unverified

38.4K

Without canonical credit

of 47.3K · 19% have detected canonical

52.6K unwrapped

Metadata coverage

repo → publication funnel

Projects in this portfolio47,337100%

with any publication linkage16,32734%

with canonical paper detected8,98319%

distinct canonical works7,27815%

canonical

9,821

mentions

20,443

paper

6,070

155

Of 47,337 projects in this portfolio, 31,010 (66%) have no detected publication linkage of any kind. These gaps are part of the story — software metadata in the wild is often missing.

Top recognized work

see all →

Most-cited publications representing software in this portfolio — the academic credit going to these projects. Items marked "detection gap" are likely portfolio software whose canonical link our pipeline failed to record.

1.
Matplotlib: A 2D Graphics Environment
37,869 citations · canonical for 4 repos · 10.1109/mcse.2007.55
2.
SciPy 1.0: fundamental algorithms for scientific computing in Python
detection gap
35,898 citations · should be canonical for scipy · 10.1038/s41592-019-0686-2
3.
Cutadapt removes adapter sequences from high-throughput sequencing reads
35,388 citations · 10.14806/ej.17.1.200
4.
Array programming with NumPy
detection gap
20,849 citations · should be canonical for numpy · 10.1038/s41586-020-2649-2
5.
Conducting Meta-Analyses inRwith themetaforPackage
18,023 citations · 10.18637/jss.v036.i03
6.
PyTorch: An Imperative Style, High-Performance Deep Learning Library
detection gap
16,163 citations · should be canonical for pytorch · 10.48550/arxiv.1912.01703
7.
Astropy: A community Python package for astronomy
detection gap
13,743 citations · should be canonical for astropy · 10.1051/0004-6361/201322068
8.
VSEARCH: a versatile open source tool for metagenomics
10,849 citations · 10.7717/peerj.2584
9.
MultiQC: summarize analysis results for multiple tools and samples in a single report
10,132 citations · canonical for 5 repos · 10.1093/bioinformatics/btw354
10.
<scp>UCSF ChimeraX</scp>: Structure visualization for researchers, educators, and developers
9,675 citations · 10.1002/pro.3943

External foundational dependencies

Upstream tools the portfolio depends on whose home repos are not in this portfolio. The citation counts here belong to the cited work — they show what these projects are built on, not what this portfolio is cited for.

1.
R: A Language and Environment for Statistical Computing
352,818 citations · used by 31 repos · 10.32614/r.manuals
2.
Deep Residual Learning for Image Recognition
216,704 citations · used by 1 repo · 10.1109/cvpr.2016.90
3.
Random Forests
121,070 citations · used by 2 repos · 10.1023/a:1010933404324
4.
Fitting Linear Mixed-Effects Models Using lme4
82,522 citations · used by 1 repo · 10.18637/jss.v067.i01
5.
Image quality assessment: from error visibility to structural similarity
54,507 citations · used by 1 repo · 10.1109/tip.2003.819861
6.
Highly accurate protein structure prediction with AlphaFold
42,869 citations · used by 2 repos · 10.1038/s41586-021-03819-2
7.
limma powers differential expression analyses for RNA-sequencing and microarray studies
41,776 citations · used by 2 repos · 10.1093/nar/gkv007
8.
Support-vector networks
39,967 citations · used by 1 repo · 10.1007/bf00994018
9.
DADA2: High-resolution sample inference from Illumina amplicon data
35,072 citations · used by 3 repos · 10.1038/nmeth.3869
10.
Human-level control through deep reinforcement learning
29,134 citations · used by 1 repo · 10.1038/nature14236

People & places

Bridge contributors

43,664

people contribute to 2+ projects in this portfolio · 36% of all contributors

Top citing institutions

Centre National de la Recherche Scientifique(FR)26,054
Chinese Academy of Sciences(CN)13,125
Harvard University(US)10,597
University of Oxford(GB)10,148
University of Cambridge(GB)8,499

Explore Full Interactive Graph

Impact

369.6K

Total Citations

316.6K

Citing Papers

26.8K

Linked Publications

301.6K

Software Dependents

1.8M

Citing Authors

50.4K

Citing Institutions

Biochemistry, Genetics...

Top Citing Field

	Portfolio	Citing
Domains	4	4
Fields	26	26
Subfields	233	252
Topics	2322	4410

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Dependencies

640.9K

Total Dependencies

Ecosystems

1.6K

Research SW Links

1.5K

Hidden Found

Ecosystem	Packages
pypi	302562
actions	120512
conda	81082
npm	55957

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Community

36450 items at risk — review sustainability

132.9K

Total People

Retention Rate

27.7%

Intl. Collaboration

513 pubs · 35937 repos

At Risk

	Pubs	Repos
Core	1404	...
Active	2100	120508
Bus Factor	-	1

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MCP Ecosystem

52644 entities have no MCP wrapper — potential funding gaps

52.6K

Unwrapped Entities

52.7K

Portfolio Entities

440

Wrapping Servers

100%

Gap Rate

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