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Dependencies
25
Software Dependencies (Direct)
147
Software Dependencies (Transitive)
952
Software Mentioned in Papers
200
Software in Cited Papers
34,807
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
32.5K(83%)
npm
2.5K(6%)
actions
2.3K(6%)
pypi
762(2%)
go
650(2%)
conda
397(1%)
docker
100(0%)
maven
29(0%)
cargo
4(0%)
rubygems
3(0%)
Depth Distribution
Direct (layer 1)
34.8K(88%)
Transitive (layer 2)
909(2%)
Transitive (layer 3)
420(1%)
Deep (layer 4+)
365(1%)
Unknown
3.0K(8%)
Dependency Types & Detection
Dependency Types
runtime
37.8K(96%)
dev
1.6K(4%)
build
90(0%)
test
20(0%)
Detection Methods
manifest_parsing
39.5K(100%)
symbol_analysis
48(0%)
Languages
R
2.8K(88%)
HTML
99(3%)
C++
94(3%)
TeX
70(2%)
C
60(2%)
Python
19(1%)
JavaScript
13(0%)
Other
30(1%)
Licenses
Unknown
2.6K
other
516
gpl-3.0
260
mit
193
gpl-2.0
48
apache-2.0
38
artistic-2.0
29
Other
58
39,471 declared, 48 discovered
39471
Declared (39471)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
34,811
Direct (layer 1)
909
Transitive (layer 2)
420
Transitive (layer 3)
365
Deep (layer 4+)
3,014
Unknown
Security Advisories
No security advisories found for portfolio dependencies.
Package Health
Health Score Distribution
Not Scored
41(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 | 1373 repos |
| r | cran | direct | declared | - | 0 | 1365 repos |
| rmarkdown | cran | direct | declared | - | 0 | 1178 repos |
| methods | cran | direct | declared | - | 0 | 1006 repos |
| biocstyle | cran | direct | declared | - | 0 | 947 repos |
| testthat | cran | direct | declared | - | 0 | 928 repos |
| stats | cran | direct | declared | - | 0 | 861 repos |
| utils | cran | direct | declared | - | 0 | 757 repos |
| ggplot2 | cran | direct | declared | - | 0 | 727 repos |
| s4vectors | cran | direct | declared | - | 0 | 521 repos |
| dplyr | cran | direct | declared | - | 0 | 514 repos |
| summarizedexperiment | cran | direct | declared | - | 0 | 475 repos |
| biocgenerics | cran | direct | declared | - | 0 | 458 repos |
| genomicranges | cran | direct | declared | - | 0 | 411 repos |
| grdevices | cran | direct | declared | - | 0 | 372 repos |
| iranges | cran | direct | declared | - | 0 | 364 repos |
| actions/checkout | actions | direct | declared | - | 0 | 345 repos |
| graphics | cran | direct | declared | - | 0 | 340 repos |
| biobase | cran | direct | declared | - | 0 | 327 repos |
| r-lib/actions/setup-r | actions | direct | declared | - | 0 | 282 repos |
Computed 7/28/2026, 10:52:22 AM across 3766 repositories