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Dependencies
25
Software Dependencies (Direct)
99
Software Dependencies (Transitive)
952
Software Mentioned in Papers
200
Software in Cited Papers
34,386
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.
Via Reference Chain (depth 2)
Repos found one level deeper in citation chains.
Software Mentions in Seed Papers
| Software | Papers ▼ | Mapped |
|---|---|---|
| bioconductor | 32 | unmapped |
| r | 24 | unmapped |
| ensembl | 14 | unmapped |
| code | 14 | unmapped |
| github | 13 | mapped |
| limma | 12 | unmapped |
| script | 8 | unmapped |
| bowtie | 7 | unmapped |
| r package | 7 | unmapped |
| samtools | 7 | unmapped |
| deseq2 | 7 | unmapped |
| edger | 6 | unmapped |
| linux | 6 | unmapped |
| star | 6 | unmapped |
| scripts | 6 | unmapped |
| python | 6 | mapped |
| chimeraviz | 5 | unmapped |
| sva | 4 | unmapped |
| stata | 4 | unmapped |
| gsea | 4 | unmapped |
What Software Do Referenced Papers Use?
Software mentioned in papers that seed papers reference.
| Software | Ref. Papers ▼ | Linked |
|---|---|---|
| r | 141 | unlinked |
| bioconductor | 101 | unlinked |
| code | 59 | unlinked |
| scripts | 51 | unlinked |
| ensembl | 50 | unlinked |
| seurat | 42 | unlinked |
| limma | 39 | unlinked |
| python | 38 | linked |
| script | 37 | unlinked |
| linux | 37 | unlinked |
| github | 33 | linked |
| edger | 32 | unlinked |
| bowtie | 31 | unlinked |
| deseq2 | 30 | unlinked |
| star | 25 | unlinked |
| ggplot | 24 | linked |
| deseq 2 | 23 | unlinked |
| scanpy | 22 | unlinked |
| r package | 22 | unlinked |
| matlab | 22 | unlinked |
Ecosystem & Depth
Ecosystem Distribution
cran
32.4K(90%)
actions
2.3K(6%)
pypi
746(2%)
conda
397(1%)
docker
72(0%)
maven
29(0%)
cargo
4(0%)
npm
3(0%)
rubygems
3(0%)
Depth Distribution
Direct (layer 1)
34.4K(95%)
Transitive (layer 2)
909(3%)
Transitive (layer 3)
420(1%)
Deep (layer 4+)
365(1%)
Unknown
30(0%)
Dependency Types & Detection
Dependency Types
runtime
36.0K(100%)
build
62(0%)
test
11(0%)
dev
3(0%)
Detection Methods
manifest_parsing
36.1K(100%)
symbol_analysis
48(0%)
36,066 declared, 48 discovered
36066
Declared (36066)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% |
| syntaxnet-with-tensorflow | pypi | gcc | 100% |
| xgboost-cpu | pypi | gcc | 100% |
| xgboost-cu13 | pypi | gcc | 100% |
| xgboost | pypi | gcc | 100% |
| syntaxnet | pypi | gcc | 100% |
| syntaxnet | pypi | glibc | 100% |
| xgboost | pypi | glibc | 100% |
| xgboost-cpu | pypi | glibc | 100% |
| syntaxnet-with-tensorflow | pypi | glibc | 100% |
| xgboost-cu13 | pypi | glibc | 100% |
| pysam | 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
34,390
Direct (layer 1)
909
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
29(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 | 1367 repos |
| r | cran | direct | declared | - | 0 | 1360 repos |
| rmarkdown | cran | direct | declared | - | 0 | 1173 repos |
| methods | cran | direct | declared | - | 0 | 1000 repos |
| biocstyle | cran | direct | declared | - | 0 | 942 repos |
| testthat | cran | direct | declared | - | 0 | 925 repos |
| stats | cran | direct | declared | - | 0 | 858 repos |
| utils | cran | direct | declared | - | 0 | 753 repos |
| ggplot2 | cran | direct | declared | - | 0 | 723 repos |
| s4vectors | cran | direct | declared | - | 0 | 518 repos |
| dplyr | cran | direct | declared | - | 0 | 511 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 | 370 repos |
| iranges | cran | direct | declared | - | 0 | 362 repos |
| actions/checkout | actions | direct | declared | - | 0 | 343 repos |
| graphics | cran | direct | declared | - | 0 | 336 repos |
| biobase | cran | direct | declared | - | 0 | 327 repos |
| r-lib/actions/setup-r | actions | direct | declared | - | 0 | 280 repos |
Computed 7/12/2026, 7:25:05 AM across 3765 repositories