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Arvindiyer merged 2 commits into from
Jul 11, 2026
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Update citation nature genetics #8

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def6571
Update citation to published Nature Genetics article
Arvindiyer Jul 10, 2026
e139627
Remove compiled objects from repository
Arvindiyer Jul 11, 2026
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5 changes: 4 additions & 1 deletion .gitignore
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Expand Up @@ -12,4 +12,7 @@ src/*.so
src/*.o
.*
!/.gitignore
!/.github
!/.githubsrc/*.o

@coderabbitai coderabbitai Bot Jul 11, 2026

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🎯 Functional Correctness | 🟠 Major | ⚡ Quick win

Fix the object-file ignore pattern.

!/.githubsrc/*.o targets a nonexistent .githubsrc path and negates the rule instead of ignoring object files under src/. Consequently, src/*.o artifacts can still be committed.

-!/.githubsrc/*.o
+src/*.o

If nested build outputs are possible, use src/**/*.o instead.

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
!/.githubsrc/*.o
src/*.o
🤖 Prompt for AI Agents 
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In @.gitignore at line 15, Correct the object-file ignore rule in .gitignore:
replace the negated nonexistent .githubsrc pattern with an ignore pattern for
object files under src/, using src/*.o or src/**/*.o if nested build outputs are
possible.

src/*.so
src/*.dll
src/*.dylib
1 change: 1 addition & 0 deletions NEWS.md
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Expand Up @@ -10,6 +10,7 @@
* Expanded test coverage with `test-gam_utils.R`.
* Repository migrated: development moved from personal branches to [CSOgroup/SelectSim](https://github.com/CSOgroup/SelectSim); `dev` branch merged into `main` for initial public release.
* Bumped version to 0.1.6 across all source files
* Updated citation (`inst/CITATION`, `README`) to the published Nature Genetics article: Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *Nature Genetics*. doi:10.1038/s41588-026-02661-4

# SelectSim 0.0.1.3

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4 changes: 2 additions & 2 deletions README.Rmd
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Expand Up @@ -28,7 +28,7 @@ The method accounts for heterogeneous tumor types, tissue specificities, and dis

This package accompanies the manuscript:

> Iyer A, Mina M, Petrovic M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *TBD*. doi: *TBD*
> Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *Nature Genetics*. doi: [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)

## Installation

Expand Down Expand Up @@ -78,7 +78,7 @@ Full documentation and vignettes are available at <https://csogroup.github.io/Se

If you use SelectSim in your research, please cite:

> Iyer A, Mina M, Petrovic M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *TBD*. doi: *TBD*
> Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *Nature Genetics*. doi: [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)

You can also run `citation("SelectSim")` inside R for a formatted reference.

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14 changes: 8 additions & 6 deletions README.md
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Expand Up @@ -28,9 +28,10 @@ frequency-stratified FDR control generated via simulation.

This package accompanies the manuscript:

> Iyer A, Mina M, Petrovic M, Ciriello G (2026). Evolving patterns of
> co-mutations from tumor initiation to metastatic progression. *TBD*.
> doi: *TBD*
> Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026).
> Evolving patterns of co-mutations from tumor initiation to metastatic
> progression. *Nature Genetics*. doi:
> [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)

## Installation

Expand Down Expand Up @@ -83,9 +84,10 @@ Full documentation and vignettes are available at

If you use SelectSim in your research, please cite:

> Iyer A, Mina M, Petrovic M, Ciriello G (2026). Evolving patterns of
> co-mutations from tumor initiation to metastatic progression. *TBD*.
> doi: *TBD*
> Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026).
> Evolving patterns of co-mutations from tumor initiation to metastatic
> progression. *Nature Genetics*. doi:
> [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)

You can also run `citation("SelectSim")` inside R for a formatted
reference.
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15 changes: 9 additions & 6 deletions inst/CITATION
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Expand Up @@ -5,16 +5,19 @@ bibentry(
title = "Evolving patterns of co-mutations from tumor initiation to metastatic progression",
author = c(
person("Arvind", "Iyer"),
person("Marco", "Mina"),
person("Miljan", "Petrovic"),
person("Debora", "Sesia"),
person("Luca", "Nanni"),
person("Marco", "Mina"),
person("Giovanni","Ciriello")
),
journal = "TBD",
journal = "Nature Genetics",
year = "2026",
doi = "", # fill in DOI once assigned
url = "https://github.com/CSOgroup/SelectSim",
doi = "10.1038/s41588-026-02661-4",
url = "https://doi.org/10.1038/s41588-026-02661-4",
textVersion = paste(
"Iyer A, Mina M, Petrovic M, Ciriello G (2026).",
"Evolving patterns of co-mutations from tumor initiation to metastatic progression."
"Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026).",
"Evolving patterns of co-mutations from tumor initiation to metastatic progression.",
"Nature Genetics. doi:10.1038/s41588-026-02661-4"
)
)
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