Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (4.0%) to scientific vocabulary
Repository
test
Basic Info
- Host: GitHub
- Owner: victorfrnak
- Language: PHP
- Default Branch: master
- Size: 14.8 MB
Statistics
- Stars: 1
- Watchers: 0
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
github code repo for fRNAkenseq (raven.anr.udel.edu) login with CyVerse credentials
Copyright 2019 Allen Hubbard
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Owner
- Login: victorfrnak
- Kind: user
- Repositories: 1
- Profile: https://github.com/victorfrnak
Citation (citations.php)
Dachwan K, Pertea G.,Trapnell, C., Pimental, H., Kelly, R., Salzberg S.L. “TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions”. Genome Biology. 2013 <br><br>
Trapnell, C., Hendrickson, D.G., Sauvageau, M., Goff, L., Rinn, J.L., Pachter, L. Differential Analysis of Gene Regulation at Transcript Resolution with RNA-seq. Nature Biotechnology 31:46-53 (2013) <br><br>
Anders, S. Theodor, P Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics Vol. 31 no. 2 2015, pages 166–169 <br><br>
Li, H. Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Marth, G., Abecasis, Durbin, R. 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15:25(16):2078-2079 <br><br>
Goff L, Trapnell C and Kelley D (2013). cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.. R package version 2.10.0. <br><br>
Trapnell, C., Hendrickson, D.G., Sauvageau, M., Goff, L., Rinn, J.L., Pachter, L. Differential Analysis of Gene Regulation at Transcript Resolution with RNA-seq. Nature Biotechnology 31:46-53 (2013) <br><br>
Hardcastle, T.J. Kelly, K.A. baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 2010. 11:422 <br><br>
Robinson, M.D., McCarthy, D.J., Smyth, G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010. Jan 1:28(1):139-140. <br><br>
Love, M. Huber, W., Anders, S. “Moderated Estimation of Fold Change and Dispersion for RNA-Seq with DESeq2”. Genome Biology. 2014, 15:550. <br><br>
http://dwheelerau.com/2014/02/17/how-to-use-deseq2-to-analyse-rnaseq-data/
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