circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

Science Score: 57.0%

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CITATION.cff file
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codemeta.json file
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DOI references
Found 21 DOI reference(s) in README
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Scientific vocabulary similarity
Low similarity (7.6%) to scientific vocabulary

Keywords

bioinformatics circrna circrna-pipeline circrna-prediction circular-rna genomics mirna mirna-targets nextflow nf-core ngs pipeline rna-seq workflow

Keywords from Contributors

metagenomics smrna-seq small-rna workflows pipelines microbiome pacbio qiime2 rrna taxonomic-classification

Last synced: 4 months ago · JSON representation ·

Repository

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

Basic Info

Host: GitHub
Owner: nf-core
License: mit
Language: Nextflow
Default Branch: dev
Homepage: https://nf-co.re/circrna
Size: 90.4 MB

Statistics

Stars: 57
Watchers: 128
Forks: 32
Open Issues: 20
Releases: 0

Topics

bioinformatics circrna circrna-pipeline circrna-prediction circular-rna genomics mirna mirna-targets nextflow nf-core ngs pipeline rna-seq workflow

Created almost 5 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

Introduction

nf-core/circrna is a bioinformatics pipeline to analyse total RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming, back-splice junction (BSJ) detection, annotation, quantification and miRNA target prediction of circular RNAs.

The pipeline is still under development, but the BSJ detection and quantification steps are already implemented and functional. The following features are planned to be implemented soon:

Isoform-level circRNA detection and quantification
circRNA-miRNA interaction analysis using SPONGE and spongEffects
Improved downstream analyses

If you want to contribute, feel free to create an issue or pull request on the GitHub repository or join the Slack channel.

Pipeline summary

Metro Map

Raw read QC (FastQC)
Adapter trimming (Trim Galore!)
BSJ detection
circRNA annotation
- Based on a GTF file
- Based on database files (if provided)
Extract circRNA sequences and build circular transcriptome
Merge circular transcriptome with linear transcriptome derived from provided GTF
Quantification of combined circular and linear transcriptome
- psirc-quant
miRNA binding affinity analysis (only if the mature parameter is provided)
- Normalizes miRNA expression (only if the mirna_expression parameter is provided)
- Binding site prediction
- miRanda
- TargetScan
- Perform majority vote on binding sites
- Compute correlations between miRNA and transcript expression levels (only if the mirna_expression parameter is provided)
Statistical tests (only if the phenotype parameter is provided)
- CircTest
MultiQC report MultiQC

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

csv title="samplesheet.csv" sample,fastq_1,fastq_2 CONTROL,CONTROL_R1.fastq.gz,CONTROL_R2.fastq.gz TREATMENT,TREATMENT_R1.fastq.gz,TREATMENT_R2.fastq.gz

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

Now, you can run the pipeline using:

bash nextflow run nf-core/circrna \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR>

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

bash nextflow run nf-core/circrna \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR>

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

Credits

nf-core/circrna was originally written by Barry Digby. It was later refactored, extended and improved by Nico Trummer.

We thank the following people for their extensive assistance in the development of this pipeline (in alphabetical order):

Acknowledgements

SFI

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #circrna channel (you can join with this invite).

Citations

nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs.

Barry Digby, Stephen P. Finn, & Pilib Ó Broin

BMC Bioinformatics 24, 27 (2023) doi: 10.1186/s12859-022-05125-8

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

Owner

Name: nf-core
Login: nf-core
Kind: organization
Email: core@nf-co.re

Website: http://nf-co.re
Twitter: nf_core
Repositories: 84
Profile: https://github.com/nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Citation (CITATIONS.md)

# nf-core/circrna: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/)

  > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.

- [Bowtie](https://doi.org/10.1186/gb-2009-10-3-r25)

  > Langmead, B., Trapnell, C., Pop, M. et al., 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25. doi: 10.1186/gb-2009-10-3-r25

- [Bowtie2](https:/dx.doi.org/10.1038/nmeth.1923)

  > Langmead, B. and Salzberg, S. L. 2012 Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), p. 357–359. doi: 10.1038/nmeth.1923.

- [BWA](https://www.ncbi.nlm.nih.gov/pubmed/19451168/)

  > Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18. PubMed PMID: 19451168; PubMed Central PMCID: PMC2705234.

- [CIRCexplorer2](https://doi.org/10.1101/gr.202895.115)

  > Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, Zhang J, Chen LL, Yang L. (2016). Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016 Sep;26(9):1277-87.

- [circRNA finder](https://doi.org/10.1016/j.celrep.2014.10.062)

  > Westholm, J.O., Lai, E.C., et al. (2016). Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation Westholm et al. Cell Reports.

- [CIRIquant](https://doi.org/10.1038/s41467-019-13840-9)

  > Zhang, J., Chen, S., Yang, J. et al. (2020). Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nat Commun 11, 90.

- [DCC](https://doi.org/10.1093/bioinformatics/btv656)

  > Jun Cheng, Franziska Metge, Christoph Dieterich, (2016). Specific identification and quantification of circular RNAs from sequencing data, Bioinformatics, 32(7), 1094–1096.

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [find circ](https://doi.org/10.1038/nature11928)

  > Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S. D., Gregersen, L. H., Munschauer, M., Loewer, A., Ziebold, U., Landthaler, M., Kocks, C., le Noble, F., & Rajewsky, N. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 495(7441), 333–338.

- [GATK](https://pubmed.ncbi.nlm.nih.gov/20644199/)

  > McKenna A, Hanna M, Banks E, et al.: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19. PubMed PMID: 20644199; PubMed Central PMCID: PMC2928508.

- [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/)

  > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. PubMed PMID: 31375807.

- [MapSplice2](https://doi.org/10.1093/nar/gkq622)

  > Wang, K., Liu J., et al. (2010) MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery, Nucleic Acids Research, 38(18), 178.

- [miRanda](https://doi.org/10.1186/gb-2003-5-1-r1)

  > Enright, A.J., John, B., Gaul, U. et al. (2003). MicroRNA targets in Drosophila. Genome Biol 5, R1.

- [find circ](https://doi.org/10.1038/nature11928)

  > Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S. D., Gregersen, L. H., Munschauer, M., Loewer, A., Ziebold, U., Landthaler, M., Kocks, C., le Noble, F., & Rajewsky, N. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 495(7441), 333–338.

- [GATK](https://pubmed.ncbi.nlm.nih.gov/20644199/)

  > McKenna A, Hanna M, Banks E, et al.: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19. PubMed PMID: 20644199; PubMed Central PMCID: PMC2928508.

- [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/)

  > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. PubMed PMID: 31375807.

- [MapSplice2](https://doi.org/10.1093/nar/gkq622)

  > Wang, K., Liu J., et al. (2010) MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery, Nucleic Acids Research, 38(18), 178.

- [miRanda](https://doi.org/10.1186/gb-2003-5-1-r1)

  > Enright, A.J., John, B., Gaul, U. et al. (2003). MicroRNA targets in Drosophila. Genome Biol 5, R1.

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

- [R](https://www.R-project.org/)

  > R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

  - [biomaRt](https://doi.org/10.1038/nprot.2009.97)

    > Durinck S, Spellman PT, Birney E, Huber W. (2009). Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc. 4(8):1184-91.

  - [circlize](https://doi.org/10.1093/bioinformatics/btu393)

    > Zuguang Gu, Lei Gu, Roland Eils, Matthias Schlesner, Benedikt Brors (2014). circlize implements and enhances circular visualization in R , Bioinformatics, 30,(19) 2811–2812.

  - [DESeq2](https://doi.org/10.1186/s13059-014-0550-8)

    > Love, M.I., Huber, W. & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550.

  - [EnhancedVolcano](https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html)

    > Blighe K, Rana S, Lewis M (2020). EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling.

  - [ggplot2](https://ggplot2.tidyverse.org)

    > Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4.

  - [ggpubr](https://rpkgs.datanovia.com/ggpubr/)

    > Kassambara A. (2020). ggpubr: 'ggplot2' Based Publication Ready Plots.

  - [ihw](https://doi.org/10.1038/nmeth.3885)

    > Ignatiadis, N., Klaus, B., Zaugg, J. et al. (2016). Data-driven hypothesis weighting increases detection power in genome-scale multiple testing. Nat Methods 13, 577–580.

  - [PCAtools](https://bioconductor.org/packages/release/bioc/html/PCAtools.html)

    > Blighe K, Lun A (2020). PCAtools: PCAtools: Everything Principal Components Analysis.

  - [pheatmap](https://cran.r-project.org/package=pheatmap)

    > Kolde, R. (2019) Pretty Heatmaps.

  - [pvclust](https://doi.org/10.1093/bioinformatics/btl117)

    > Suzuki R., Shimodaira H., (2006). Pvclust: an R package for assessing the uncertainty in hierarchical clustering, Bioinformatics, 22(12), 1540–1542.

- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)

  > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.

- [Segemehl](https://doi.org/10.1371/journal.pcbi.1000502)

  > Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J: "Fast mapping of short sequences with mismatches, insertions and deletions using index structures", PLoS Comput Biol (2009) vol. 5 (9) pp. e1000502.

- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/)

  > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.

- [StringTie2](https://pubmed.ncbi.nlm.nih.gov/31842956/)

  > Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2 Genome Biol. 2019 Dec 16;20(1):278. doi: 10.1186/s13059-019-1910-1. PubMed PMID: 31842956; PubMed Central PMCID: PMC6912988.

- [TargetScan](https://doi.org/10.7554/elife.05005)

  > Agarwal V, Bell GW, Nam JW, Bartel DP. (2015). Predicting effective microRNA target sites in mammalian mRNAs. Elife, 4:e05005.

- [ViennaRNA](https://doi.org/10.1186/1748-7188-6-26)

  > Lorenz, R., Bernhart, S.H., Höner zu Siederdissen, C. et al. (2011). ViennaRNA Package 2.0. Algorithms Mol Biol 6, 26.

## Test data References

> Cao D. An autoregulation loop in fust-1 for circular RNA regulation in Caenorhabditis elegans. Genetics. 2021 Nov 5;219(3):iyab145. doi: 10.1093/genetics/iyab145. PMID: 34740247; PMCID: PMC8570788.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

GitHub Events

Total

Issues event: 24
Watch event: 11
Delete event: 20
Member event: 1
Issue comment event: 53
Push event: 95
Pull request event: 43
Pull request review event: 2
Fork event: 9
Create event: 23

Last Year

Issues event: 24
Watch event: 11
Delete event: 20
Member event: 1
Issue comment event: 53
Push event: 95
Pull request event: 43
Pull request review event: 2
Fork event: 9
Create event: 23

Committers

Last synced: about 2 years ago

All Time

Total Commits: 1,020
Total Committers: 6
Avg Commits per committer: 170.0
Development Distribution Score (DDS): 0.025

Past Year

Commits: 208
Committers: 4
Avg Commits per committer: 52.0
Development Distribution Score (DDS): 0.058

Top Committers

Name	Email	Commits
Barry digby	b**7@g**m	994
nf-core-bot	c**e@n**e	18
Alexander Peltzer	a**r@g**m	5
Ben Whittle	7**w@u**m	1
MaxUlysse	m**a@g**m	1
kevinmenden	k**n@t**e	1

Committer Domains (Top 20 + Academic)

t-online.de: 1 nf-co.re: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 70
Total pull requests: 124
Average time to close issues: 4 months
Average time to close pull requests: about 1 month
Total issue authors: 25
Total pull request authors: 16
Average comments per issue: 1.89
Average comments per pull request: 1.31
Merged pull requests: 76
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 15
Pull requests: 16
Average time to close issues: 18 days
Average time to close pull requests: 7 days
Issue authors: 6
Pull request authors: 3
Average comments per issue: 0.67
Average comments per pull request: 0.75
Merged pull requests: 10
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

nictru (25)
BarryDigby (7)
ZabalaAitor (4)
csittz (3)
luciazifcakova (2)
guillaumecharbonnier (2)
bkbx (2)
pnolabs (2)
yshen16 (2)
mazzalab (2)
MariekeVromman (2)
ianyfchang (2)
bioShaun (2)
xfk274280 (1)
Fabian-Boehm (1)

Pull Request Authors

nictru (44)
BarryDigby (34)
nf-core-bot (29)
MariekeVromman (5)
jfy133 (2)
xfk274280 (2)
WalshKieran (2)
Dibassow (1)
chaesee1 (1)
bj-w (1)
Fabian-Boehm (1)
mweyrich28 (1)
MrNiro (1)
drpatelh (1)
maxulysse (1)

Top Labels

Issue Labels

bug (34) enhancement (20) feature-request (7) first-timers-only (5) WIP (1) DSL2 (1) documentation (1)

Pull Request Labels

bug (6) enhancement (5) documentation (1) feature-request (1)

Dependencies

.github/workflows/awsfulltest.yml actions

actions/upload-artifact v3 composite
nf-core/tower-action v3 composite

.github/workflows/awstest.yml actions

actions/upload-artifact v3 composite
nf-core/tower-action v3 composite

.github/workflows/branch.yml actions

mshick/add-pr-comment v1 composite

.github/workflows/ci.yml actions

actions/checkout v3 composite
nf-core/setup-nextflow v1 composite

.github/workflows/fix-linting.yml actions

actions/checkout v3 composite
actions/setup-node v3 composite

.github/workflows/linting.yml actions

actions/checkout v3 composite
actions/setup-node v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite
mshick/add-pr-comment v1 composite
nf-core/setup-nextflow v1 composite
psf/black stable composite

.github/workflows/linting_comment.yml actions

dawidd6/action-download-artifact v2 composite
marocchino/sticky-pull-request-comment v2 composite

modules/nf-core/bowtie/align/meta.yml cpan

modules/nf-core/bowtie/build/meta.yml cpan

modules/nf-core/bowtie2/align/meta.yml cpan

modules/nf-core/bowtie2/build/meta.yml cpan

modules/nf-core/bwa/index/meta.yml cpan

modules/nf-core/cat/fastq/meta.yml cpan

modules/nf-core/circexplorer2/annotate/meta.yml cpan

modules/nf-core/circexplorer2/parse/meta.yml cpan

modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan

modules/nf-core/fastqc/meta.yml cpan

modules/nf-core/hisat2/align/meta.yml cpan

modules/nf-core/hisat2/build/meta.yml cpan

modules/nf-core/hisat2/extractsplicesites/meta.yml cpan

modules/nf-core/miranda/meta.yml cpan

modules/nf-core/multiqc/meta.yml cpan

modules/nf-core/samtools/index/meta.yml cpan

modules/nf-core/samtools/sort/meta.yml cpan

modules/nf-core/samtools/view/meta.yml cpan

modules/nf-core/segemehl/align/meta.yml cpan

modules/nf-core/segemehl/index/meta.yml cpan

modules/nf-core/star/align/meta.yml cpan

modules/nf-core/star/genomegenerate/meta.yml cpan

modules/nf-core/stringtie/stringtie/meta.yml cpan

modules/nf-core/trimgalore/meta.yml cpan

pyproject.toml pypi

circrna

Science Score: 57.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Introduction

Pipeline summary

Usage

Pipeline output

Pipeline output

Credits

Acknowledgements

Contributions and Support

Citations

Owner

Citation (CITATIONS.md)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

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Top Authors

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Issue Labels

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Dependencies