[PRE REVIEW]: graphsim: An R package for simulating gene expression data from graph structures of biological pathways

[whedon]

Submitting author: @TomKellyGenetics (S. Thomas Kelly)
Repository: https://github.com/TomKellyGenetics/graphsim
Version: 0.1.2
Editor: @majensen
Reviewers: @rcannood, @corybrunson
Managing EiC: Kevin M. Moerman

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PDF failed to compile for issue #2137 with the following error:

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'

[Kevin-Mattheus-Moerman]

@openjournals/dev can you see what is preventing paper compilation here?

[whedon]

Reference check summary:

OK DOIs

- 10.1186/gb-2014-15-2-r29 is OK
- 10.1186/1752-0509-3-41 is OK
- 10.1093/bioinformatics/btm639 is OK
- 10.1515/jib-2017-0027 is OK
- 10.1093/imanum/22.3.329 is OK
- 10.1186/s13062-015-0086-1 is OK
- 10.1101/gad.11.13.1748 is OK
- 10.1093/bioinformatics/btp174 is OK
- 10.1093/bioinformatics/btu736 is OK
- 10.1093/hmg/ddu309 is OK
- 10.1007/BF01386390 is OK
- 10.1177/1558689812454457 is OK
- 10.1111/j.1651-2227.2006.00178.x is OK
- 10.1124/jpet.103.064824 is OK
- 10.1016/j.cell.2009.02.024 is OK
- 10.1103/PhysRevLett.87.198701 is OK
- 10.1039/C3MB25589A is OK
- 10.1186/gb-2010-11-3-r25 is OK
- 10.1186/1471-2407-14-552 is OK
- 10.1016/j.fob.2012.04.003 is OK
- 10.1200/JCO.2008.18.1370 is OK
- 10.1093/nar/gkt1102 is OK
- 10.1093/bioinformatics/btl633 is OK
- 10.1093/annonc/mdg486 is OK
- 10.1093/hmg/ddp046 is OK
- 10.1001/jama.297.21.2360 is OK
- 10.1371/journal.pgen.1003254 is OK
- 10.1186/1479-5876-7-43 is OK
- 10.1038/nrd3374 is OK
- 10.1158/1078-0432.ccr-13-3116 is OK
- 10.1016/j.ddtec.2013.12.002 is OK
- 10.1038/nrg3899 is OK
- 10.1016/j.cell.2015.11.015 is OK
- 10.1186/gb-2004-5-10-r80 is OK

MISSING DOIs

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- https://doi.org/10.1186/1471-2105-8-s6-s5 may be missing for title: Inferring cellular networks–a review
- https://doi.org/10.1038/nprot.2017.149 may be missing for title: Exponential scaling of single-cell RNA-seq in the past decade
- https://doi.org/10.1038/nrg.2016.87 may be missing for title: Network biology concepts in complex disease comorbidities
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- https://doi.org/10.1109/msp.2007.273053 may be missing for title: Finding module-based gene networks with state-space models - Mining high-dimensional and short time-course gene expression data
- https://doi.org/10.3892/ijo.2012.1744 may be missing for title: Molecular features of triple negative breast cancer cells by genome-wide gene expression profiling analysis
- https://doi.org/10.1186/s12967-017-1197-5 may be missing for title: Transcriptomic profiling and quantitative high-throughput (qHTS) drug screening of CDH1 deficient hereditary diffuse gastric cancer (HDGC) cells identify treatment leads for familial gastric cancer
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- https://doi.org/10.1186/bcr2887 may be missing for title: Three interrelated themes in current breast cancer research: gene addiction, phenotypic plasticity, and cancer stem cells
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- https://doi.org/10.1093/nar/gkl811 may be missing for title: CancerGenes: a gene selection resource for cancer genome projects
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- https://doi.org/10.1038/ng.2983 may be missing for title: Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer
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- https://doi.org/10.1186/bcr2899 may be missing for title: Analysis of tumor environmental response and oncogenic pathway activation identifies distinct basal and luminal features in HER2-related breast tumor subtypes
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- https://doi.org/10.1038/ncomms11908 may be missing for title: Erratum: The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes
- https://doi.org/10.1038/nature10983 may be missing for title: The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
- https://doi.org/10.1038/nbt.1637 may be missing for title: Comparative assessment of methods for aligning multiple genome sequences
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- https://doi.org/10.1038/nrg3394 may be missing for title: Reuse of public genome-wide gene expression data
- https://doi.org/10.1093/nar/gks1174 may be missing for title: ArrayExpress update–trends in database growth and links to data analysis tools
- https://doi.org/10.1016/j.ctrv.2011.11.005 may be missing for title: Molecular biology in breast cancer: intrinsic subtypes and signaling pathways
- https://doi.org/10.1200/jco.20.5.1260 may be missing for title: Outcome of preventive surgery and screening for breast and ovarian cancer in BRCA mutation carriers
- https://doi.org/10.1186/gb-2007-8-5-r76 may be missing for title: Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors
- https://doi.org/10.1634/theoncologist.2010-s5-39 may be missing for title: Molecular stratification of triple-negative breast cancers
- https://doi.org/10.1261/rna.1947110 may be missing for title: Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression
- https://doi.org/10.1373/clinchem.2015.249623 may be missing for title: Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants
- https://doi.org/10.1371/journal.pone.0103917 may be missing for title: A method for quantitative analysis of standard and high-throughput qPCR expression data based on input sample quantity
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- https://doi.org/10.1186/bcr326 may be missing for title: Update on HER-2 as a target for cancer therapy: herceptin in the clinical setting
- https://doi.org/10.1016/j.yane.2012.02.046 may be missing for title: Hallmarks of cancer: the next generation
- https://doi.org/10.1038/452788b may be missing for title: James Watson’s genome sequenced at high speed
- https://doi.org/10.1038/44413 may be missing for title: Wellcome funds cancer database
- https://doi.org/10.1073/pnas.70.12.3581 may be missing for title: The Nucleotide Sequence of the lac Operator
- https://doi.org/10.1158/1535-7163.mct-14-0845 may be missing for title: Functional Genetic Screen Identifies Increased Sensitivity to WEE1 Inhibition in Cells with Defects in Fanconi Anemia and HR Pathways
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- https://doi.org/10.1371/journal.pgen.1004120 may be missing for title: Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli
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- https://doi.org/10.1186/gm99 may be missing for title: Synthetic Lethality: a framework for the development of wiser cancer therapeutics
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- https://doi.org/10.1016/j.ccr.2014.08.008 may be missing for title: DAISY: Picking Synthetic Lethals from Cancer Genomes
- https://doi.org/10.1038/bjc.1997.523 may be missing for title: E-cadherin inactivation in lobular carcinoma in situ of the breast: an early event in tumorigenesis
- https://doi.org/10.1101/cshperspect.a003129 may be missing for title: Involvement of Members of the Cadherin Superfamily in Cancer
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INVALID DOIs

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[Kevin-Mattheus-Moerman]

@csoneson @majensen @will-rowe are you able to edit this submission?

[TomKellyGenetics]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[TomKellyGenetics]

References corrected.

@whedon generate pdf

[Kevin-Mattheus-Moerman]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[Kevin-Mattheus-Moerman]

@TomKellyGenetics I think you need to use only the command message text and no other text.

[TomKellyGenetics]

@Kevin-Mattheus-Moerman Thanks, I was thinking to try that. Wasn't sure how long it was meant to take. That's fixed the bibliography.

[TomKellyGenetics]

Suggested reviewers (by appropriate expertise):

biswapriyamisra
kozo2
camillescott
rcannood
corybrunson

[Kevin-Mattheus-Moerman]

@csoneson @majensen @will-rowe can you edit this one?

[Kevin-Mattheus-Moerman]

@whedon invite @csoneson as editor

[whedon]

@csoneson has been invited to edit this submission.

[Kevin-Mattheus-Moerman]

@whedon invite @majensen as editor

[whedon]

@majensen has been invited to edit this submission.

[Kevin-Mattheus-Moerman]

@whedeon invite @will-rowe as editor

[majensen]

@whedon assign @majensen as editor

[whedon]

OK, the editor is @majensen

[majensen]

@corybrunson would you be able to review this submission to JOSS? Thanks for considering!

[majensen]

@rcannood would appreciate your review of this submission to JOSS. Please let me know -- thanks!

[rcannood]

Sure!

…

On Wed, 11 Mar 2020, 02:49 Mark Jensen, ***@***.***> wrote: @rcannood <https://github.com/rcannood> would appreciate your review of this submission to JOSS <https://joss.theoj.org>. Please let me know -- thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2137?email_source=notifications&email_token=AAEHFKVKNWQTPI3IX6NKN6DRG3UZ7A5CNFSM4LBAISW2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEON2HQI#issuecomment-597402561>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAEHFKUVMS5DBA2JHCQOVTTRG3UZ7ANCNFSM4LBAISWQ> .

[majensen]

@whedon assign @rcannood as reviewer

[whedon]

OK, @rcannood is now a reviewer

[corybrunson]

@majensen not this week, but i would be able to next week! If that's OK, then i'm glad to be assigned.

[arfon]

@TomKellyGenetics - you might want to truncate your bibtex entries to only those that are cited in the JOSS paper to prevent Whedon responses like this one: #2137 (comment)

[majensen]

@majensen not this week, but i would be able to next week! If that's OK, then i'm glad to be assigned.

That would be excellent @corybrunson -- very much appreciated!

[majensen]

@whedon add @corybrunson as reviewer

[whedon]

OK, @corybrunson is now a reviewer

[majensen]

@whedon start review

[whedon]

OK, I've started the review over in #2161.

[majensen]

Thanks @rcannood and @corybrunson for stepping up to review this interesting work by @TomKellyGenetics - please join us at #2161!