Dependencies

943

Software Dependencies (Direct)

412

Software Dependencies (Transitive)

6,999

Software Mentioned in Papers

200

Software in Cited Papers

89,034

Declared Dependencies

From manifests

1,523

Discovered (Hidden)

Symbol + wrapper analysis

504

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	155
deepin-community/matplotlib	155
swe-bench-repos/matplotlib__matplotlib	155
matplotlib/matplotlib	155
suxianmin/polio	84
julialang/julia	84
azzaare/julia-1	84
jainecassimiro/melhorias-ca-ticas-no-c-digo-julia	84
enzocipriani/language-julia	84
mpds-ws23-cws/nextflow	41
nextflow-io/nextflow	41
sultanabubaker/sast-gradle-project	41
adamrtalbot/nextflow	41
tylerdurden120/data_platform	36
scikit-image/scikit-image	36
deepin-community/skimage	36
swe-gym-raw/scikit-image__scikit-image	36
pydata/xarray	35
swe-bench-repos/pydata__xarray	35
flamingbear/original-fork-xarray	35

Via Reference Chain (depth 2)

Repos found one level deeper in citation chains.

Repository	Ref. Papers ▼
salilab/imp	22
chfeder/turbulence_generator	20
seandavi/geoquery	17
bioc/geoquery	17
allenai/allennlp	13
hpparvi/ldtk	13
hoffmangroup/segway	13
hamzashoaib7781/allennlp	13
swe-train/allenai__allennlp	13
vida-nyu/reprozip	12
sciencefair2018/deepfri-explainability	8
flatironinstitute/deepfri	8
bioinf-mcb/metagenomic-deepfri	8
decodegenetics/lrcaller	7
ivanek/gviz	6
alok-ai-lab/pydeepinsight	6
bioconductor-source/gviz	6
bsc-wdc/compss	6
salilab/modloop	6
bioc/gviz	6

Software Mentions in Seed Papers

Software	Papers ▼	Mapped
code	183	unmapped
github	127	mapped
linux	119	unmapped
scripts	96	unmapped
script	90	unmapped
windows	88	unmapped
matlab	86	unmapped
python	85	mapped
library	84	mapped
scipy	77	mapped
numpy	77	mapped
matplotlib	55	mapped
package	51	unmapped
r	49	unmapped
pypi	43	unmapped
scikit-learn	37	mapped
api	37	unmapped
latex	37	unmapped
pytorch	35	mapped
macos	33	unmapped

What Software Do Referenced Papers Use?

Software mentioned in papers that seed papers reference.

Software	Ref. Papers ▼	Linked
code	507	unlinked
scripts	392	unlinked
r	380	unlinked
python	379	linked
github	347	linked
script	318	unlinked
matlab	318	unlinked
linux	317	unlinked
windows	217	unlinked
scipy	216	linked
numpy	209	linked
matplotlib	189	linked
library	140	linked
samtools	135	unlinked
scikit-learn	130	linked
package	128	unlinked
blast	128	unlinked
pytorch	127	linked
tensorflow	125	linked
latex	120	unlinked

Ecosystem & Depth

Ecosystem Distribution

pypi

302.6K(52%)

actions

120.5K(21%)

conda

81.1K(14%)

npm

56.0K(10%)

rubygems

8.8K(2%)

docker

3.5K(1%)

cran

2.6K(0%)

1.2K(0%)

julia

1.0K(0%)

Other

2.6K(0%)

Depth Distribution

Direct (layer 1)

89.0K(14%)

Transitive (layer 2)

170.3K(27%)

Transitive (layer 3)

182.8K(29%)

Deep (layer 4+)

139.0K(22%)

Unknown

59.8K(9%)

Dependency Types & Detection

Dependency Types

runtime

612.5K(96%)

dev

23.3K(4%)

build

3.2K(1%)

test

1.8K(0%)

Detection Methods

manifest_parsing

639.4K(100%)

symbol_analysis

1.5K(0%)

Languages

Python

14.9K(40%)

HTML

5.1K(13%)

JavaScript

4.4K(12%)

Jupyter Notebook

3.6K(9%)

1.9K(5%)

C++

1.6K(4%)

Julia

1.4K(4%)

Other

4.8K(13%)

Licenses

mit

11.2K

Unknown

11.2K

apache-2.0

8.0K

other

7.6K

gpl-3.0

3.1K

bsd-3-clause

1.8K

agpl-3.0

1.5K

Other

2.5K

639,354 declared, 1,523 discovered

639354

Declared (639354)Discovered (1523)

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%	244
gcc(runtime)	library	100%	195
libstdcxx(runtime)	library	100%	165
openblas(linear_algebra)	library	100%	42
openmp(runtime)	library	100%	38
zlib(compression)	library	100%	35
cuda(gpu)	library	100%	28
curand(gpu)	library	100%	20
cusolver(gpu)	library	100%	20
cufft(gpu)	library	100%	20
cudnn(gpu)	library	100%	20
cusparse(gpu)	library	100%	19
nccl(gpu)	library	100%	18
nvrtc(gpu)	library	100%	18
gfortran(runtime)	library	100%	18
quadmath(math)	library	100%	14
cutensor(gpu)	library	100%	13
c(other)	library	100%	12
torch(other)	library	100%	12
nvToolsExt(gpu)	library	100%	12

Transitive Chain Depth

88,987

Direct (layer 1)

170,301

Transitive (layer 2)

182,798

Transitive (layer 3)

138,958

Deep (layer 4+)

59,833

Unknown

Security Advisories

No security advisories found for portfolio dependencies.

Package Health

Health Score Distribution

Not Scored

110(100%)

System Library Health

Name	Category	Health	Funded	Deps ▼
glibc	runtime	-	unfunded	1742
gcc	runtime	-	unfunded	1406
libstdcxx	runtime	-	unfunded	1373
zlib	compression	-	unfunded	1212
openblas	linear_algebra	-	unfunded	1207
gfortran	runtime	-	unfunded	1181
quadmath	math	-	unfunded	1177
boringssl	crypto	-	unfunded	1140
libpng	image	-	unfunded	1132
zmq	other	-	unfunded	1130
libsodium	crypto	-	unfunded	1130
sodium	other	-	unfunded	1130
openssl	crypto	-	unfunded	1129
libjpeg-turbo	image	-	unfunded	1128
libwebp	image	-	unfunded	1128
sharpyuv	other	-	unfunded	1128
xz	compression	-	unfunded	1127
zstd	compression	-	unfunded	1126
libtiff	image	-	unfunded	1124
openjp	other	-	unfunded	1123

Most widely used packages across portfolio repositories.

Shared only (50)

Package	Ecosystem	Type	Detection	Health	Used By ▼
actions/checkout	actions	direct	declared	-	3510 repos
actions/upload-artifact	actions	direct	declared	-	2447 repos
actions/setup-python	actions	direct	declared	-	2098 repos
codecov/codecov-action	actions	direct	declared	-	2076 repos
actions/setup-node	actions	direct	declared	-	1966 repos
pyyaml	pypi	direct	declared	-	1715 repos
actions/cache	actions	direct	declared	-	1707 repos
numpy	pypi	direct	declared	-	1560 repos
docker/setup-qemu-action	actions	direct	declared	-	1529 repos
beautifulsoup4	pypi	direct	declared	-	1491 repos
pandas	pypi	direct	declared	-	1451 repos
matplotlib	pypi	direct	declared	-	1432 repos
pytest	pypi	direct	declared	-	1410 repos
scipy	pypi	direct	declared	-	1403 repos
sphinx	pypi	direct	declared	-	1389 repos
pypa/gh-action-pypi-publish	actions	direct	declared	-	1384 repos
packaging	pypi	direct	declared	-	1383 repos
actions/download-artifact	actions	direct	declared	-	1365 repos
typing-extensions	pypi	direct	declared	-	1363 repos
setuptools	pypi	direct	declared	-	1351 repos

Computed 9/8/2026, 4:17:20 PM across 47496 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