rnalysis

Description

rnalysis website

Python-based software for analyzing RNA sequencing data.

Environment Modules

Run module spider rnalysis to find out what environment modules are available for this application.

Environment Variables

• HPC_RNALYSIS__DIR - installation directory
• HPC_RNALYSIS_BIN - executable directory

Citation

If you publish research that uses rnalysis you have to cite it as follows:

• Teichman, G., Cohen, D., Ganon, O., Dunsky, N., Shani, S., Gingold, H., and Rechavi, O. (2023). RNAlysis: analyze your RNA sequencing data without writing a single line of code. BMC Biology, 21, 74. https://doi.org/10.1186/s12915-023-01574-6

If you use the CutAdapt adapter trimming tool in your research, please cite:

• Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), pp. 10-12. https://doi.org/10.14806/ej.17.1.200

If you use the kallisto RNA sequencing quantification tool in your research, please cite:

• Bray, N., Pimentel, H., Melsted, P. et al. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 34, 525–527 (2016). https://doi.org/10.1038/nbt.3519

If you use the bowtie2 aligner in your research, please cite:

• Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012 94 9, 357–359. https://doi.org/10.1038/nmeth.1923

If you use the ShortStack aligner in your research, please cite:

• Axtell, MJ. (2013). ShortStack: Comprehensive annotation and quantification of small RNA genes. RNA 19:740-751. https://doi.org/10.1261/rna.035279.112

If you use the DESeq2 differential expression tool in your research, please cite:

• Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. https://doi.org/10.1186/s13059-014-0550-8

If you use the Limma-Voom differential expression pipeline in your research, please cite:

• Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47–e47. https://doi.org/10.1093/nar/gkv007
• Law, C.W., Chen, Y., Shi, W., and Smyth, G.K. (2014). Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 15, 1–17. https://doi.org/10.1186/gb-2014-15-2-r29

If you use the HDBSCAN clustering feature in your research, please cite:

• L. McInnes, J. Healy, S. Astels, hdbscan: Hierarchical density based clustering In: Journal of Open Source Software, The Open Journal, volume 2, number 11. 2017 https://doi.org/10.1371/journal.pcbi.0030039

If you use the XL-mHG single-set enrichment test in your research, please cite:

• Eden, E., Lipson, D., Yogev, S., and Yakhini, Z. (2007). Discovering Motifs in Ranked Lists of DNA Sequences. PLOS Comput. Biol. 3, e39. https://doi.org/10.1371/journal.pcbi.0030039
• Wagner, F. (2017). The XL-mHG test for gene set enrichment. ArXiv. https://doi.org/10.48550/arXiv.1507.07905

Categories

sequencing, biology