From ef3acdb082ed7cb52266b12247f613aa7fe4158e Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Tue, 2 Mar 2021 16:14:29 -0600 Subject: [PATCH] Add new references to doc --- docs/references.md | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/docs/references.md b/docs/references.md index 4ea1690..77c124d 100644 --- a/docs/references.md +++ b/docs/references.md @@ -9,9 +9,6 @@ 3. **BDBag**: * D'Arcy, M., Chard, K., Foster, I., Kesselman, C., Madduri, R., Saint, N., & Wagner, R.. 2019. Big Data Bags: A Scalable Packaging Format for Science. Zenodo. doi:[10.5281/zenodo.3338725](http://doi.org/10.5281/zenodo.3338725). -4. **RSeQC**: - * Wang, L., Wang, S., Li, W. 2012 RSeQC: quality control of RNA-seq experiments. Bioinformatics. Aug 15;28(16):2184-5. doi:[10.1093/bioinformatics/bts356](https://doi.org/10.1093/bioinformatics/bts356). - 5. **trimgalore**: * trimgalore [https://github.com/FelixKrueger/TrimGalore](https://github.com/FelixKrueger/TrimGalore) @@ -27,15 +24,24 @@ 9. **featureCounts**: * Liao, Y., Smyth, G.K., Shi, W. 2014 featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. Apr 1;30(7):923-30. doi:[10.1093/bioinformatics/btt656](https://doi.org/10.1093/bioinformatics/btt656). -10. **R**: - * R Core Team 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL:[http://www.R-project.org/](http://www.R-project.org/). - 11. **deeptools**: * RamÃrez, F., D. P. Ryan, B. Grüning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dündar, and T. Manke. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research 44: W160-165. doi:[10.1093/nar/gkw257](http://dx.doi.org/10.1093/nar/gkw257) +11. **Seqtk**: + * Seqtk [https://github.com/lh3/seqtk](https://github.com/lh3/seqtk) + +10. **R**: + * R Core Team 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL:[http://www.R-project.org/](http://www.R-project.org/). + 12. **FastQC** * FastQC [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) +12. **SeqWho** + * SeqWho [https://git.biohpc.swmed.edu/s181649/seqwho](https://git.biohpc.swmed.edu/s181649/seqwho) + +4. **RSeQC**: + * Wang, L., Wang, S., Li, W. 2012 RSeQC: quality control of RNA-seq experiments. Bioinformatics. Aug 15;28(16):2184-5. doi:[10.1093/bioinformatics/bts356](https://doi.org/10.1093/bioinformatics/bts356). + 13. **MultiQC**: * Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354) -- GitLab