Dependencies

604

Software Dependencies (Direct)

393

Software Dependencies (Transitive)

4,025

Software Mentioned in Papers

200

Software in Cited Papers

116,684

Declared Dependencies

From manifests

1,015

Discovered (Hidden)

Symbol + wrapper analysis

496

System Libraries

With Known Vulns

None detected

What Software Does This Research Build On?

Via Cited DOIs (depth 1)

Repos whose canonical DOI paper is directly cited by seed papers.

Repository	Seed Papers ▼
neha1010/matplot	75
deepin-community/matplotlib	75
swe-bench-repos/matplotlib__matplotlib	75
matplotlib/matplotlib	75
suxianmin/polio	36
julialang/julia	36
azzaare/julia-1	36
jainecassimiro/melhorias-ca-ticas-no-c-digo-julia	36
enzocipriani/language-julia	36
mpds-ws23-cws/nextflow	20
nextflow-io/nextflow	20
sultanabubaker/sast-gradle-project	20
adamrtalbot/nextflow	20
tylerdurden120/data_platform	16
scikit-image/scikit-image	16
deepin-community/skimage	16
swe-gym-raw/scikit-image__scikit-image	16
pydata/xarray	14
swe-bench-repos/pydata__xarray	14
flamingbear/original-fork-xarray	14

Via Reference Chain (depth 2)

Repos found one level deeper in citation chains.

Repository	Ref. Papers ▼
salilab/imp	16
hpparvi/ldtk	12
wviechtb/metafor	12
joonyeol-sim/ompl	10
ompl/ompl	10
seandavi/geoquery	9
hoffmangroup/segway	9
bioc/geoquery	9
pyomo/pyomo	7
vida-nyu/reprozip	7
gajahterban/pyomo	7
zzygith/pyomorevised	7
moldyn/hp35-desres	7
decodegenetics/lrcaller	7
deeplabcut/deeplabcut-live	6
pymc-devs/pymc3	6
salilab/modloop	6
pymc-devs/pymc	6
openforcefield/openff-bespokefit	6
oren11/isca	5

Software Mentions in Seed Papers

Software	Papers ▼	Mapped
code	100	unmapped
github	82	mapped
linux	63	unmapped
scripts	58	unmapped
script	52	unmapped
windows	50	unmapped
python	49	mapped
matlab	41	unmapped
numpy	41	mapped
scipy	40	mapped
library	35	mapped
matplotlib	28	mapped
r	27	unmapped
package	26	unmapped
api	24	unmapped
pypi	23	unmapped
latex	22	unmapped
scikit-learn	21	mapped
pytorch	20	mapped
macos	19	unmapped

What Software Do Referenced Papers Use?

Software mentioned in papers that seed papers reference.

Software	Ref. Papers ▼	Linked
code	317	unlinked
scripts	244	unlinked
python	241	linked
r	231	unlinked
github	230	linked
script	203	unlinked
matlab	200	unlinked
linux	198	unlinked
scipy	141	linked
windows	140	unlinked
numpy	138	linked
matplotlib	130	linked
blast	88	unlinked
samtools	88	unlinked
scikit-learn	82	linked
java	80	unlinked
package	80	unlinked
tensorflow	79	linked
bioconductor	77	unlinked
library	76	linked

Ecosystem & Depth

Ecosystem Distribution

pypi

579.4K(38%)

npm

526.3K(34%)

actions

206.6K(13%)

conda

154.8K(10%)

rubygems

29.8K(2%)

docker

7.8K(1%)

packagist

6.5K(0%)

6.2K(0%)

cran

5.2K(0%)

Other

13.2K(1%)

Depth Distribution

Direct (layer 1)

116.7K(7%)

Transitive (layer 2)

341.3K(21%)

Transitive (layer 3)

369.7K(22%)

Deep (layer 4+)

275.5K(17%)

Unknown

555.0K(33%)

Dependency Types & Detection

Dependency Types

runtime

1.4M(87%)

dev

201.5K(12%)

build

6.8K(0%)

test

1.9K(0%)

Detection Methods

manifest_parsing

1.7M(100%)

symbol_analysis

1.0K(0%)

Languages

Python

4.2K(36%)

C++

1.2K(11%)

Jupyter Notebook

1.1K(9%)

HTML

806(7%)

JavaScript

730(6%)

677(6%)

PHP

547(5%)

Other

2.5K(21%)

Licenses

Unknown

7.8K

mit

3.5K

other

2.1K

apache-2.0

1.1K

bsd-3-clause

870

gpl-3.0

846

gpl-2.0

358

Other

789

1,657,151 declared, 1,015 discovered

1657151

Declared (1657151)Discovered (1015)

Wrapper-Detected Pairs

Language packages that wrap underlying system libraries.

Package	Ecosystem	System Library	Confidence ▼
ortools	pypi	absl_base	100%
ortools	pypi	absl_city	100%
ortools	pypi	absl_civil_time	100%
ortools	pypi	absl_cord_internal	100%
ortools	pypi	absl_cordz_functions	100%
ortools	pypi	absl_cordz_handle	100%
ortools	pypi	absl_cordz_info	100%
ortools	pypi	absl_crc_cord_state	100%
ortools	pypi	absl_crc_cpu_detect	100%
ortools	pypi	absl_crc_internal	100%
ortools	pypi	absl_crc32c	100%
ortools	pypi	absl_debugging_internal	100%
ortools	pypi	absl_decode_rust_punycode	100%
ortools	pypi	absl_demangle_internal	100%
ortools	pypi	absl_demangle_rust	100%
ortools	pypi	absl_die_if_null	100%
ortools	pypi	absl_examine_stack	100%
ortools	pypi	absl_exponential_biased	100%
ortools	pypi	absl_flags_commandlineflag_internal	100%
ortools	pypi	absl_flags_config	100%

Symbol-Analysis Discoveries

Undeclared dependencies found via binary/symbol analysis.

Target	Type	Confidence ▼	Sources
glibc(runtime)	library	100%	131
gcc(runtime)	library	100%	108
libstdcxx(runtime)	library	100%	99
openblas(linear_algebra)	library	100%	33
openmp(runtime)	library	100%	25
zlib(compression)	library	100%	23
cufft(gpu)	library	100%	20
curand(gpu)	library	100%	20
cuda(gpu)	library	100%	19
cusolver(gpu)	library	100%	18
cusparse(gpu)	library	100%	18
cudnn(gpu)	library	100%	18
nccl(gpu)	library	100%	18
nvrtc(gpu)	library	100%	18
cutensor(gpu)	library	100%	13
gfortran(runtime)	library	100%	12
nvToolsExt(gpu)	library	100%	12
amdhip(gpu)	library	100%	7
quadmath(math)	library	100%	7
libpng(image)	library	100%	5

Transitive Chain Depth

116,695

Direct (layer 1)

341,288

Transitive (layer 2)

369,702

Transitive (layer 3)

275,514

Deep (layer 4+)

554,967

Unknown

Security Advisories

No security advisories found for portfolio dependencies.

Package Health

Health Score Distribution

Not Scored

453(100%)

System Library Health

Name	Category	Health	Funded	Deps ▼
glibc	runtime	-	unfunded	2834
gcc	runtime	-	unfunded	2560
libstdcxx	runtime	-	unfunded	2540
zlib	compression	-	unfunded	2344
boringssl	crypto	-	unfunded	2330
openblas	linear_algebra	-	unfunded	2309
libsodium	crypto	-	unfunded	2296
zmq	other	-	unfunded	2296
sodium	other	-	unfunded	2296
libpng	image	-	unfunded	2293
sharpyuv	other	-	unfunded	2286
libjpeg-turbo	image	-	unfunded	2286
libwebp	image	-	unfunded	2286
gfortran	runtime	-	unfunded	2286
quadmath	math	-	unfunded	2281
xz	compression	-	unfunded	2280
openssl	crypto	-	unfunded	2280
brotli	compression	-	unfunded	2278
libtiff	image	-	unfunded	2277
xcb	other	-	unfunded	2277

Most widely used packages across portfolio repositories.

Shared only (50)

Package	Ecosystem	Type	Detection	Health	Used By ▼
actions/checkout	actions	direct	declared	-	3454 repos
actions/setup-python	actions	direct	declared	-	2909 repos
actions/upload-artifact	actions	direct	declared	-	2799 repos
sphinx	pypi	direct	declared	-	2634 repos
actions/download-artifact	actions	direct	declared	-	2603 repos
packaging	pypi	direct	declared	-	2599 repos
pypa/gh-action-pypi-publish	actions	direct	declared	-	2599 repos
docker/setup-qemu-action	actions	direct	declared	-	2592 repos
typing-extensions	pypi	direct	declared	-	2592 repos
actions/setup-node	actions	direct	declared	-	2587 repos
actions/cache	actions	direct	declared	-	2575 repos
jinja2	pypi	direct	declared	-	2568 repos
markupsafe	pypi	direct	declared	-	2567 repos
colorama	pypi	direct	declared	-	2564 repos
sphinx-rtd-theme	pypi	direct	declared	-	2564 repos
codecov/codecov-action	actions	direct	declared	-	2562 repos
setuptools	pypi	direct	declared	-	2555 repos
tomli	pypi	direct	declared	-	2554 repos
pytest	pypi	direct	declared	-	2548 repos
platformdirs	pypi	direct	declared	-	2542 repos

Computed 7/24/2026, 6:00:54 PM across 18630 repositories

Dependencies

Dependencies At A Glance

Research Software Dependencies

Via Cited DOIs (depth 1)

Via Reference Chain (depth 2)

Software Mentions in Seed Papers

Supply Chain Composition

Ecosystem Distribution

Depth Distribution

Dependency Types

Detection Methods

Repository Composition

Languages

Licenses

Hidden Dependencies — What PRSM Discovered

Wrapper-Detected Pairs

Symbol-Analysis Discoveries

Transitive Chain Depth

Risk & Health

Health Score Distribution

System Library Health

Top Dependencies

System Libraries