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Dependencies
2
Software Dependencies (Direct)
5
Software Dependencies (Transitive)
911
Software Mentioned in Papers
2,355
Software in Cited Papers
34,272
Declared Dependencies
From manifests
48
Discovered (Hidden)
Symbol + wrapper analysis
60
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 ▼ |
|---|---|
| nextflow-io/nextflow | 1 |
| sympy/sympy | 1 |
Via Reference Chain (depth 2)
Repos found one level deeper in citation chains.
| Repository | Ref. Papers ▼ |
|---|---|
| matplotlib/matplotlib | 6 |
| ilastik/ilastik | 2 |
| scikit-image/scikit-image | 2 |
| pandas-dev/pandas | 1 |
| brainglobe/brainrender | 1 |
Software Mentions in Seed Papers
| Software | Papers ▼ | Mapped |
|---|---|---|
| bioconductor | 31 | unmapped |
| r | 23 | unmapped |
| ensembl | 14 | unmapped |
| code | 13 | unmapped |
| github | 12 | mapped |
| limma | 12 | unmapped |
| bowtie | 7 | unmapped |
| script | 7 | unmapped |
| samtools | 7 | unmapped |
| deseq2 | 7 | unmapped |
| edger | 6 | unmapped |
| linux | 6 | unmapped |
| r package | 6 | unmapped |
| star | 6 | unmapped |
| python | 6 | mapped |
| chimeraviz | 5 | unmapped |
| scripts | 5 | unmapped |
| stata | 4 | unmapped |
| biomart | 4 | unmapped |
| windows | 4 | unmapped |
What Software Do Referenced Papers Use?
Software mentioned in papers that seed papers reference.
| Software | Ref. Papers ▼ | Linked |
|---|---|---|
| r | 62 | unlinked |
| bioconductor | 51 | unlinked |
| ensembl | 32 | unlinked |
| code | 27 | unlinked |
| seurat | 24 | unlinked |
| limma | 22 | unlinked |
| scripts | 22 | unlinked |
| script | 21 | unlinked |
| bowtie | 19 | unlinked |
| linux | 19 | unlinked |
| deseq2 | 18 | unlinked |
| edger | 18 | unlinked |
| star | 16 | unlinked |
| tophat | 16 | unlinked |
| github | 16 | linked |
| python | 15 | linked |
| deseq 2 | 13 | unlinked |
| scanpy | 12 | unlinked |
| samtools | 12 | unlinked |
| windows | 11 | unlinked |
Ecosystem & Depth
Ecosystem Distribution
cran
32.3K(90%)
actions
2.3K(6%)
pypi
737(2%)
conda
397(1%)
docker
69(0%)
maven
29(0%)
cargo
4(0%)
npm
3(0%)
rubygems
3(0%)
Depth Distribution
Direct (layer 1)
34.3K(95%)
Transitive (layer 2)
905(3%)
Transitive (layer 3)
420(1%)
Deep (layer 4+)
365(1%)
Unknown
30(0%)
Dependency Types & Detection
Dependency Types
runtime
35.9K(100%)
build
60(0%)
test
11(0%)
dev
3(0%)
Detection Methods
manifest_parsing
35.9K(100%)
symbol_analysis
48(0%)
35,948 declared, 48 discovered
35948
Declared (35948)Discovered (48)
Wrapper-Detected Pairs
Language packages that wrap underlying system libraries.
| Package | Ecosystem | System Library | Confidence ▼ |
|---|---|---|---|
| pysam | pypi | brotli | 100% |
| pysam | pypi | bzip2 | 100% |
| pysam | pypi | cbcftools | 100% |
| pysam | pypi | chtslib | 100% |
| pysam | pypi | com_err | 100% |
| pysam | pypi | crypt | 100% |
| pysam | pypi | csamtools | 100% |
| pysam | pypi | curl | 100% |
| pysam | pypi | cutils | 100% |
| xgboost-cu13 | pypi | gcc | 100% |
| syntaxnet-with-tensorflow | pypi | gcc | 100% |
| xgboost-cpu | pypi | gcc | 100% |
| syntaxnet | pypi | gcc | 100% |
| xgboost | pypi | gcc | 100% |
| syntaxnet-with-tensorflow | pypi | glibc | 100% |
| xgboost | pypi | glibc | 100% |
| xgboost-cu13 | pypi | glibc | 100% |
| syntaxnet | pypi | glibc | 100% |
| pysam | pypi | glibc | 100% |
| xgboost-cpu | pypi | glibc | 100% |
Symbol-Analysis Discoveries
Undeclared dependencies found via binary/symbol analysis.
| Target | Type | Confidence ▼ | Sources |
|---|---|---|---|
| glibc(runtime) | library | 100% | 6 |
| gcc(runtime) | library | 100% | 5 |
| libstdcxx(runtime) | library | 100% | 5 |
| openmp(runtime) | library | 100% | 3 |
| chtslib(runtime) | library | 100% | 1 |
| com_err(other) | library | 100% | 1 |
| crypt(other) | library | 100% | 1 |
| csamtools(runtime) | library | 100% | 1 |
| curl(networking) | library | 100% | 1 |
| cutils(runtime) | library | 100% | 1 |
| gssapi_krb(other) | library | 100% | 1 |
| idn(other) | library | 100% | 1 |
| k5crypto(crypto) | library | 100% | 1 |
| keyutils(other) | library | 100% | 1 |
| krb5support(other) | library | 100% | 1 |
| lber(other) | library | 100% | 1 |
| ldap(other) | library | 100% | 1 |
| nghttp2(networking) | library | 100% | 1 |
| openssl(crypto) | library | 100% | 1 |
| pcre2(other) | library | 100% | 1 |
Transitive Chain Depth
34,276
Direct (layer 1)
905
Transitive (layer 2)
420
Transitive (layer 3)
365
Deep (layer 4+)
30
Unknown
Security Advisories
No security advisories found for portfolio dependencies.
Package Health
Health Score Distribution
Not Scored
27(100%)
System Library Health
| Name | Category | Health | Funded | Deps ▼ |
|---|---|---|---|---|
| glibc | runtime | - | unfunded | 9 |
| libstdcxx | runtime | - | unfunded | 8 |
| gcc | runtime | - | unfunded | 8 |
| brotli | compression | - | unfunded | 4 |
| zlib | compression | - | unfunded | 4 |
| k5crypto | crypto | - | unfunded | 4 |
| openssl | crypto | - | unfunded | 4 |
| krb5support | other | - | unfunded | 4 |
| xz | compression | - | unfunded | 4 |
| gssapi_krb | other | - | unfunded | 4 |
| keyutils | other | - | unfunded | 4 |
| selinux | other | - | unfunded | 4 |
| openmp | runtime | - | unfunded | 4 |
| curl | networking | - | unfunded | 4 |
| pcre2 | other | - | unfunded | 4 |
| boringssl | crypto | - | unfunded | 4 |
| com_err | other | - | unfunded | 4 |
| xcb | other | - | unfunded | 3 |
| Xau | other | - | unfunded | 3 |
| openjp | other | - | unfunded | 3 |
Most widely used packages across portfolio repositories.
| Package | Ecosystem | Type | Detection | Health | Advisories | Used By ▼ |
|---|---|---|---|---|---|---|
| knitr | cran | direct | declared | - | 0 | 1364 repos |
| r | cran | direct | declared | - | 0 | 1357 repos |
| rmarkdown | cran | direct | declared | - | 0 | 1170 repos |
| methods | cran | direct | declared | - | 0 | 1000 repos |
| biocstyle | cran | direct | declared | - | 0 | 942 repos |
| testthat | cran | direct | declared | - | 0 | 923 repos |
| stats | cran | direct | declared | - | 0 | 856 repos |
| utils | cran | direct | declared | - | 0 | 750 repos |
| ggplot2 | cran | direct | declared | - | 0 | 721 repos |
| s4vectors | cran | direct | declared | - | 0 | 518 repos |
| dplyr | cran | direct | declared | - | 0 | 508 repos |
| summarizedexperiment | cran | direct | declared | - | 0 | 473 repos |
| biocgenerics | cran | direct | declared | - | 0 | 456 repos |
| genomicranges | cran | direct | declared | - | 0 | 410 repos |
| grdevices | cran | direct | declared | - | 0 | 369 repos |
| iranges | cran | direct | declared | - | 0 | 362 repos |
| actions/checkout | actions | direct | declared | - | 0 | 339 repos |
| graphics | cran | direct | declared | - | 0 | 336 repos |
| biobase | cran | direct | declared | - | 0 | 327 repos |
| r-lib/actions/setup-r | actions | direct | declared | - | 0 | 277 repos |
Computed 4/16/2026, 9:56:11 PM across 3709 repositories