[PRE REVIEW]: OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases

[whedon]

Submitting author: @JonnyTran (Nhat Tran)
Repository: https://github.com/BioMeCIS-Lab/OpenOmics
Version: v0.8.8
Editor: @arfon
Reviewers: @arfon
Managing EiC: Arfon Smith

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Author instructions

Thanks for submitting your paper to JOSS @JonnyTran. Currently, there isn't an JOSS editor assigned to your paper.

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Editor instructions

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[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

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[arfon]

Fast-tracking this submission because it has already been reviewed in pyOpenSci/software-submission#31 (comment)

[arfon]

@whedon assign me as editor

[whedon]

OK, the editor is @arfon

[arfon]

@whedon assign @arfon as reviewer

[whedon]

OK, @arfon is now a reviewer

[arfon]

@whedon start review

[whedon]

OK, I've started the review over in #3249.

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=3.98 s (33.7 files/s, 2869.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          38           1044           1782           3615
Markdown                        21            292              0           1284
CSS                              5            197             87            982
TeX                              1             59              0            478
reStructuredText                61            426            704            127
YAML                             2             12             16             87
make                             2             24              6             78
XML                              2              0              0             71
DOS Batch                        1              8              1             27
TOML                             1              6              0             14
-------------------------------------------------------------------------------
SUM:                           134           2068           2596           6763
-------------------------------------------------------------------------------


Statistical information for the repository '90afefd9fa19eed3fd6cd13d' was
gathered on 2021/05/05.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Jonny Tran                     930         16307          11528           34.34
JonnyTran                      457         27907          24256           64.35
Nhat Tran                        2           110             82            0.24
deepsource-autofix[b            12           624            252            1.08

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Jonny Tran                 3618           22.2         10.5               11.08
JonnyTran                  2335            8.4          7.7               14.26
deepsource-autofix[b        488           78.2          2.3                0.00

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/nar/gky1079 is OK

MISSING DOIs

- 10.1093/nar/gkaa554 may be a valid DOI for title: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
- 10.1093/bioinformatics/btz133 may be a valid DOI for title: Anduril 2: upgraded large-scale data integration framework
- 10.1074/mcp.m115.052381 may be a valid DOI for title: Integration of metabolomics and transcriptomics reveals major metabolic pathways and potential biomarker involved in prostate cancer
- 10.1371/journal.pcbi.1005752 may be a valid DOI for title: mixOmics: An R package for ‘omics feature selection and multiple data integration
- 10.1186/gm186 may be a valid DOI for title: Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme
- 10.1093/nar/gkw377 may be a valid DOI for title: Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
- 10.1038/nrg3606 may be a valid DOI for title: Long non-coding RNAs: new players in cell differentiation and development
- 10.1093/nar/gkr1175 may be a valid DOI for title: NONCODE v3. 0: integrative annotation of long noncoding RNAs
- 10.1093/nar/gks915 may be a valid DOI for title: LNCipedia: a database for annotated human lncRNA transcript sequences and structures
- 10.1101/gr.132159.111 may be a valid DOI for title: The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
- 10.1093/nar/gku1173 may be a valid DOI for title: LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression
- 10.1093/nar/gky1051 may be a valid DOI for title: LncRNA2Target v2. 0: a comprehensive database for target genes of lncRNAs in human and mouse
- 10.1093/database/bav083 may be a valid DOI for title: LncReg: a reference resource for lncRNA-associated regulatory networks
- 10.1093/nar/gkq1138 may be a valid DOI for title: lncRNAdb: a reference database for long noncoding RNAs
- 10.1093/nar/gkw943 may be a valid DOI for title: DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants
- 10.1093/nar/gks1099 may be a valid DOI for title: LncRNADisease: a database for long-non-coding RNA-associated diseases
- 10.1093/nar/gkj112 may be a valid DOI for title: miRBase: microRNA sequences, targets and gene nomenclature
- 10.1093/nar/gkt1057 may be a valid DOI for title: NPInter v2. 0: an updated database of ncRNA interactions
- 10.1093/database/bav083 may be a valid DOI for title: LncReg: a reference resource for lncRNA-associated regulatory networks
- 10.1093/database/bat034 may be a valid DOI for title: lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
- 10.1093/nar/gkj147 may be a valid DOI for title: The HUGO gene nomenclature database, 2006 updates
- 10.1017/cbo9780511546198.190 may be a valid DOI for title: Scale-free networks in cell biology
- 10.1093/nar/gkv1270 may be a valid DOI for title: DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts
- 10.1093/nar/gkw1102 may be a valid DOI for title: The BioGRID interaction database: 2017 update
- 10.1093/nar/gkt1248 may be a valid DOI for title: starBase v2. 0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data
- 10.1371/journal.pcbi.1005752 may be a valid DOI for title: mixOmics: An R package for ‘omics feature selection and multiple data integration

INVALID DOIs

- None