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Dependencies
6
Software Dependencies (Direct)
5
Software Dependencies (Transitive)
440
Software Mentioned in Papers
341
Software in Cited Papers
1,396
Declared Dependencies
From manifests
461
Discovered (Hidden)
Symbol + wrapper analysis
50
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.
| Repository | Seed Papers ▼ |
|---|---|
| matplotlib/matplotlib | 7 |
| bactopia/bactopia | 4 |
| julialang/julia | 2 |
| scikit-image/scikit-image | 2 |
| ropensci/beautier | 1 |
| arviz-devs/arviz | 1 |
Via Reference Chain (depth 2)
Repos found one level deeper in citation chains.
| Repository | Ref. Papers ▼ |
|---|---|
| pybamm-team/pybamm | 2 |
| sympy/sympy | 2 |
| pymc-devs/pymc | 2 |
| pandas-dev/pandas | 1 |
| sunpy/sunpy | 1 |
Software Mentions in Seed Papers
| Software | Papers ▼ | Mapped |
|---|---|---|
| asa3p | 6 | unmapped |
| github | 6 | unmapped |
| docker | 5 | unmapped |
| fastqc | 5 | unmapped |
| spades | 5 | unmapped |
| linux | 5 | unmapped |
| quast | 5 | unmapped |
| bactopia | 5 | unmapped |
| python | 5 | unmapped |
| trimmomatic | 4 | unmapped |
| nextflow | 4 | unmapped |
| fastq | 4 | unmapped |
| tormes | 4 | unmapped |
| unicycler | 4 | unmapped |
| prokka | 4 | unmapped |
| plasmidfinder | 3 | unmapped |
| xarray | 3 | unmapped |
| card | 3 | unmapped |
| singularity | 3 | unmapped |
| roary | 3 | unmapped |
What Software Do Referenced Papers Use?
Software mentioned in papers that seed papers reference.
| Software | Ref. Papers ▼ | Linked |
|---|---|---|
| github | 5 | unlinked |
| python | 4 | unlinked |
| docker | 4 | unlinked |
| bioconda | 3 | unlinked |
| scripts | 3 | unlinked |
| scikit-learn | 3 | unlinked |
| windows | 3 | unlinked |
| cython | 3 | unlinked |
| linux | 3 | unlinked |
| unicycler | 3 | unlinked |
| matlab | 3 | unlinked |
| blast+ | 3 | unlinked |
| pypi | 3 | unlinked |
| spades | 3 | unlinked |
| blast | 3 | unlinked |
| c | 2 | unlinked |
| prodigal | 2 | unlinked |
| hmmer | 2 | unlinked |
| prokka | 2 | unlinked |
| scikit - learn | 2 | unlinked |
Ecosystem & Depth
Ecosystem Distribution
conda
1.3K(40%)
pypi
1.1K(36%)
actions
660(21%)
cran
28(1%)
npm
21(1%)
docker
14(0%)
vcpkg
2(0%)
Depth Distribution
Direct (layer 1)
1.4K(39%)
Transitive (layer 2)
1.5K(41%)
Transitive (layer 3)
699(20%)
Dependency Types & Detection
Dependency Types
runtime
3.5K(97%)
test
52(1%)
dev
45(1%)
build
14(0%)
Detection Methods
manifest_parsing
3.1K(87%)
symbol_analysis
461(13%)
Languages
Python
30(70%)
C++
5(12%)
TypeScript
2(5%)
R
2(5%)
C
1(2%)
JavaScript
1(2%)
Julia
1(2%)
Nextflow
1(2%)
Licenses
other
14
bsd-3-clause
13
mit
7
apache-2.0
5
Unknown
2
gpl-3.0
1
bsd-2-clause
1
3,110 declared, 461 discovered
3110
Declared (3110)Discovered (461)
Wrapper-Detected Pairs
Language packages that wrap underlying system libraries.
| Package | Ecosystem | System Library | Confidence ▼ |
|---|---|---|---|
| cupy-rocm-4-3 | pypi | amdhip | 100% |
| cupy-rocm-4-2 | pypi | amdhip | 100% |
| cupy-rocm-7-0 | pypi | amdhip | 100% |
| cupy-rocm-4-0 | pypi | amdhip | 100% |
| cupy-rocm-5-0 | pypi | amdhip | 100% |
| mlpack | pypi | armadillo | 100% |
| mlpack3 | pypi | armadillo | 100% |
| mlpack | pypi | arpack | 100% |
| tables | pypi | blosc | 100% |
| mlpack3 | pypi | boost_serialization | 100% |
| mlpack3 | pypi | boost_unit_test_framework | 100% |
| tables | pypi | bzip2 | 100% |
| cupy-cuda110 | pypi | cuda | 100% |
| cupy-cuda113 | pypi | cuda | 100% |
| cupy-cuda117 | pypi | cuda | 100% |
| cupy-cuda114 | pypi | cuda | 100% |
| cupy-cuda91 | pypi | cuda | 100% |
| cupy-cuda112 | pypi | cuda | 100% |
| cupy-cuda111 | pypi | cuda | 100% |
| cupy-cuda116 | pypi | cuda | 100% |
Symbol-Analysis Discoveries
Undeclared dependencies found via binary/symbol analysis.
| Target | Type | Confidence ▼ | Sources |
|---|---|---|---|
| glibc(runtime) | library | 100% | 54 |
| gcc(runtime) | library | 100% | 49 |
| libstdcxx(runtime) | library | 100% | 48 |
| openblas(linear_algebra) | library | 100% | 29 |
| openmp(runtime) | library | 100% | 20 |
| cusolver(gpu) | library | 100% | 18 |
| curand(gpu) | library | 100% | 18 |
| nvrtc(gpu) | library | 100% | 18 |
| nccl(gpu) | library | 100% | 18 |
| cusparse(gpu) | library | 100% | 18 |
| cufft(gpu) | library | 100% | 18 |
| cudnn(gpu) | library | 100% | 16 |
| cuda(gpu) | library | 100% | 15 |
| cutensor(gpu) | library | 100% | 13 |
| nvToolsExt(gpu) | library | 100% | 12 |
| gfortran(runtime) | library | 100% | 7 |
| tbb(threading) | library | 100% | 6 |
| amdhip(gpu) | library | 100% | 5 |
| hiprand(gpu) | library | 100% | 5 |
| hipsparse(gpu) | library | 100% | 5 |
Transitive Chain Depth
1,402
Direct (layer 1)
1,470
Transitive (layer 2)
699
Transitive (layer 3)
Security Advisories
No security advisories found for portfolio dependencies.
Package Health
Health Score Distribution
Not Scored
37(100%)
System Library Health
| Name | Category | Health | Funded | Deps ▼ |
|---|---|---|---|---|
| glibc | runtime | - | unfunded | 54 |
| gcc | runtime | - | unfunded | 49 |
| libstdcxx | runtime | - | unfunded | 48 |
| openblas | linear_algebra | - | unfunded | 31 |
| openmp | runtime | - | unfunded | 20 |
| cusolver | gpu | - | unfunded | 18 |
| cusparse | gpu | - | unfunded | 18 |
| cufft | gpu | - | unfunded | 18 |
| curand | gpu | - | unfunded | 18 |
| nccl | gpu | - | unfunded | 18 |
| nvrtc | gpu | - | unfunded | 18 |
| cudnn | gpu | - | unfunded | 16 |
| cuda | gpu | - | unfunded | 15 |
| cutensor | gpu | - | unfunded | 13 |
| nvToolsExt | gpu | - | unfunded | 12 |
| gfortran | runtime | - | unfunded | 7 |
| lapack | linear_algebra | - | unfunded | 6 |
| tbb | threading | - | unfunded | 6 |
| amdhip | gpu | - | unfunded | 5 |
| zlib | compression | - | unfunded | 5 |
Most widely used packages across portfolio repositories.
| Package | Ecosystem | Type | Detection | Health | Advisories | Used By ▼ |
|---|---|---|---|---|---|---|
| actions/checkout | actions | direct | declared | - | 0 | 27 repos |
| actions/upload-artifact | actions | direct | declared | - | 0 | 23 repos |
| actions/setup-python | actions | direct | declared | - | 0 | 22 repos |
| sphinx | pypi | direct | declared | - | 0 | 21 repos |
| actions/download-artifact | actions | direct | declared | - | 0 | 20 repos |
| pandas | pypi | direct | declared | - | 0 | 20 repos |
| scipy | pypi | direct | declared | - | 0 | 20 repos |
| actions/cache | actions | direct | declared | - | 0 | 19 repos |
| actions/labeler | actions | direct | declared | - | 0 | 19 repos |
| codecov/codecov-action | actions | direct | declared | - | 0 | 19 repos |
| cython | pypi | direct | declared | - | 0 | 19 repos |
| ipykernel | pypi | direct | declared | - | 0 | 19 repos |
| ipykernel | conda | direct | declared | - | 0 | 19 repos |
| ipython | pypi | direct | declared | - | 0 | 19 repos |
| matplotlib | pypi | direct | declared | - | 0 | 19 repos |
| numpy | pypi | direct | declared | - | 0 | 19 repos |
| numpydoc | pypi | direct | declared | - | 0 | 19 repos |
| pillow | pypi | direct | declared | - | 0 | 19 repos |
| pypa/cibuildwheel | actions | direct | declared | - | 0 | 19 repos |
| pyqt | conda | direct | declared | - | 0 | 19 repos |
Computed 2/22/2026, 4:43:48 PM across 43 repositories