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Dependencies
55
Software Dependencies (Direct)
27
Software Dependencies (Transitive)
442
Software Mentioned in Papers
200
Software in Cited Papers
6,926
Declared Dependencies
From manifests
536
Discovered (Hidden)
Symbol + wrapper analysis
158
System Libraries
0
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.
Via Reference Chain (depth 2)
Repos found one level deeper in citation chains.
Software Mentions in Seed Papers
| Software | Papers ▼ | Mapped |
|---|---|---|
| asa3p | 6 | unmapped |
| github | 6 | mapped |
| quast | 5 | unmapped |
| python | 5 | mapped |
| linux | 5 | unmapped |
| fastqc | 5 | unmapped |
| bactopia | 5 | mapped |
| spades | 5 | unmapped |
| docker | 5 | mapped |
| unicycler | 4 | unmapped |
| nextflow | 4 | unmapped |
| prokka | 4 | unmapped |
| matplotlib | 4 | mapped |
| tormes | 4 | unmapped |
| trimmomatic | 4 | unmapped |
| fastq | 4 | unmapped |
| java | 3 | unmapped |
| resfinder | 3 | unmapped |
| cython | 3 | mapped |
| numpy | 3 | mapped |
What Software Do Referenced Papers Use?
Software mentioned in papers that seed papers reference.
| Software | Ref. Papers ▼ | Linked |
|---|---|---|
| scripts | 21 | unlinked |
| python | 18 | linked |
| github | 17 | linked |
| blast | 17 | unlinked |
| code | 17 | unlinked |
| linux | 16 | unlinked |
| script | 13 | unlinked |
| r | 13 | unlinked |
| spades | 11 | unlinked |
| windows | 11 | unlinked |
| matlab | 11 | unlinked |
| matplotlib | 10 | linked |
| scipy | 10 | linked |
| bwa | 9 | unlinked |
| unicycler | 9 | unlinked |
| resfinder | 9 | unlinked |
| nucmer | 8 | unlinked |
| plasmidfinder | 8 | unlinked |
| numpy | 8 | linked |
| cython | 7 | linked |
Ecosystem & Depth
Ecosystem Distribution
pypi
21.2K(49%)
actions
9.3K(22%)
conda
8.3K(19%)
npm
2.8K(7%)
go
667(2%)
cran
374(1%)
docker
283(1%)
nuget
8(0%)
vcpkg
6(0%)
Other
7(0%)
Depth Distribution
Direct (layer 1)
6.9K(15%)
Transitive (layer 2)
11.4K(24%)
Transitive (layer 3)
14.8K(31%)
Deep (layer 4+)
10.5K(22%)
Unknown
3.5K(7%)
Dependency Types & Detection
Dependency Types
runtime
44.9K(95%)
dev
1.8K(4%)
build
282(1%)
test
111(0%)
Detection Methods
manifest_parsing
46.6K(99%)
symbol_analysis
536(1%)
Languages
Python
51(74%)
C++
9(13%)
R
2(3%)
C
1(1%)
Cython
1(1%)
JavaScript
1(1%)
Julia
1(1%)
Other
3(4%)
Licenses
bsd-3-clause
19
other
19
apache-2.0
16
Unknown
13
mit
7
bsd-2-clause
1
bsl-1.0
1
Other
4
46,559 declared, 536 discovered
46559
Declared (46559)Discovered (536)
Wrapper-Detected Pairs
Language packages that wrap underlying system libraries.
| Package | Ecosystem | System Library | Confidence ▼ |
|---|---|---|---|
| cupy-rocm-5-0 | pypi | amdhip | 100% |
| cupy-rocm-4-0 | pypi | amdhip | 100% |
| cupy-rocm-7-0 | pypi | amdhip | 100% |
| cupy-rocm-4-3 | pypi | amdhip | 100% |
| cupy-rocm-4-2 | pypi | amdhip | 100% |
| mlpack | pypi | armadillo | 100% |
| mlpack3 | pypi | armadillo | 100% |
| mlpack | pypi | arpack | 100% |
| tensorflow-io-nightly | pypi | avcodec | 100% |
| tensorflow-io | pypi | avcodec | 100% |
| tensorflow-io | pypi | avformat | 100% |
| tensorflow-io-nightly | pypi | avformat | 100% |
| pillow | pypi | avif | 100% |
| tensorflow-io | pypi | avutil | 100% |
| tensorflow-io-nightly | pypi | avutil | 100% |
| tables | pypi | blosc | 100% |
| friday-dlib | pypi | boost_python | 100% |
| mlpack3 | pypi | boost_serialization | 100% |
| mlpack3 | pypi | boost_unit_test_framework | 100% |
| pillow | pypi | brotli | 100% |
Symbol-Analysis Discoveries
Undeclared dependencies found via binary/symbol analysis.
| Target | Type | Confidence ▼ | Sources |
|---|---|---|---|
| glibc(runtime) | library | 100% | 66 |
| gcc(runtime) | library | 100% | 59 |
| libstdcxx(runtime) | library | 100% | 58 |
| openblas(linear_algebra) | library | 100% | 31 |
| openmp(runtime) | library | 100% | 20 |
| curand(gpu) | library | 100% | 19 |
| cusolver(gpu) | library | 100% | 19 |
| nvrtc(gpu) | library | 100% | 18 |
| cufft(gpu) | library | 100% | 18 |
| cusparse(gpu) | library | 100% | 18 |
| nccl(gpu) | library | 100% | 18 |
| cudnn(gpu) | library | 100% | 17 |
| cuda(gpu) | library | 100% | 15 |
| cutensor(gpu) | library | 100% | 13 |
| nvToolsExt(gpu) | library | 100% | 12 |
| gfortran(runtime) | library | 100% | 7 |
| zlib(compression) | library | 100% | 6 |
| tbb(threading) | library | 100% | 6 |
| rocsolver(gpu) | library | 100% | 5 |
| roctx(gpu) | library | 100% | 5 |
Transitive Chain Depth
6,933
Direct (layer 1)
11,351
Transitive (layer 2)
14,804
Transitive (layer 3)
10,490
Deep (layer 4+)
3,517
Unknown
Security Advisories
No security advisories found for portfolio dependencies.
Package Health
Health Score Distribution
Not Scored
53(100%)
System Library Health
| Name | Category | Health | Funded | Deps ▼ |
|---|---|---|---|---|
| glibc | runtime | - | unfunded | 162 |
| gcc | runtime | - | unfunded | 151 |
| libstdcxx | runtime | - | unfunded | 150 |
| openblas | linear_algebra | - | unfunded | 125 |
| gfortran | runtime | - | unfunded | 99 |
| zlib | compression | - | unfunded | 98 |
| quadmath | math | - | unfunded | 96 |
| libjpeg-turbo | image | - | unfunded | 90 |
| libpng | image | - | unfunded | 90 |
| zstd | compression | - | unfunded | 89 |
| avif | other | - | unfunded | 89 |
| Xau | other | - | unfunded | 89 |
| freetype | image | - | unfunded | 89 |
| xz | compression | - | unfunded | 89 |
| brotli | compression | - | unfunded | 89 |
| xcb | other | - | unfunded | 89 |
| libwebp | image | - | unfunded | 89 |
| lcms | other | - | unfunded | 89 |
| harfbuzz | other | - | unfunded | 89 |
| sharpyuv | other | - | unfunded | 89 |
Most widely used packages across portfolio repositories.
| Package | Ecosystem | Type | Detection | Health | Advisories | Used By ▼ |
|---|---|---|---|---|---|---|
| actions/checkout | actions | direct | declared | - | 0 | 148 repos |
| actions/upload-artifact | actions | direct | declared | - | 0 | 131 repos |
| actions/setup-python | actions | direct | declared | - | 0 | 123 repos |
| sphinx | pypi | direct | declared | - | 0 | 120 repos |
| actions/download-artifact | actions | direct | declared | - | 0 | 117 repos |
| actions/cache | actions | direct | declared | - | 0 | 116 repos |
| codecov/codecov-action | actions | direct | declared | - | 0 | 116 repos |
| urllib3 | pypi | direct | declared | - | 0 | 116 repos |
| docker/setup-qemu-action | actions | direct | declared | - | 0 | 115 repos |
| packaging | pypi | direct | declared | - | 0 | 115 repos |
| numpy | pypi | direct | declared | - | 0 | 114 repos |
| scipy | pypi | direct | declared | - | 0 | 114 repos |
| pandas | pypi | direct | declared | - | 0 | 113 repos |
| matplotlib | pypi | direct | declared | - | 0 | 112 repos |
| pyparsing | pypi | direct | declared | - | 0 | 112 repos |
| sphinx-copybutton | pypi | direct | declared | - | 0 | 112 repos |
| actions/stale | actions | direct | declared | - | 0 | 111 repos |
| cython | pypi | direct | declared | - | 0 | 111 repos |
| pillow | pypi | direct | declared | - | 0 | 111 repos |
| pytest | pypi | direct | declared | - | 0 | 111 repos |
Computed 7/28/2026, 10:07:21 AM across 447 repositories