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qSVA framework for RNA quality correction in differential expression analysis.
Jaffe AE, Tao R, Norris AL, Kealhofer M, Nellore A, Shin JH, Kim D, Jia Y, Hyde TM, Kleinman JE, Straub RE, Leek JT, Weinberger DR. Jaffe AE, et al. Among authors: nellore a. Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):7130-7135. doi: 10.1073/pnas.1617384114. Epub 2017 Jun 20. Proc Natl Acad Sci U S A. 2017. PMID: 28634288 Free PMC article.
Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce.
Nellore A, Wilks C, Hansen KD, Leek JT, Langmead B. Nellore A, et al. Bioinformatics. 2016 Aug 15;32(16):2551-3. doi: 10.1093/bioinformatics/btw177. Epub 2016 Apr 21. Bioinformatics. 2016. PMID: 27153614 Free PMC article.
RESULTS: We present a protocol and software tool for analyzing protected data in a commercial cloud. The protocol, Rail-dbGaP, is applicable to any tool running on Amazon Web Services Elastic MapReduce. The tool, Rail-RNA v0.2, is a spliced aligner for RNA-se …
RESULTS: We present a protocol and software tool for analyzing protected data in a commercial cloud. The protocol, Rail-dbGaP, …
Rail-RNA: scalable analysis of RNA-seq splicing and coverage.
Nellore A, Collado-Torres L, Jaffe AE, Alquicira-Hernández J, Wilks C, Pritt J, Morton J, Leek JT, Langmead B. Nellore A, et al. Bioinformatics. 2017 Dec 15;33(24):4033-4040. doi: 10.1093/bioinformatics/btw575. Bioinformatics. 2017. PMID: 27592709 Free PMC article.
Flexible expressed region analysis for RNA-seq with derfinder.
Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE. Collado-Torres L, et al. Among authors: nellore a. Nucleic Acids Res. 2017 Jan 25;45(2):e9. doi: 10.1093/nar/gkw852. Epub 2016 Sep 29. Nucleic Acids Res. 2017. PMID: 27694310 Free PMC article.
Reproducible RNA-seq analysis using recount2.
Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT. Collado-Torres L, et al. Among authors: nellore a. Nat Biotechnol. 2017 Apr 11;35(4):319-321. doi: 10.1038/nbt.3838. Nat Biotechnol. 2017. PMID: 28398307 Free PMC article. No abstract available.
recount3: summaries and queries for large-scale RNA-seq expression and splicing.
Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, Hansen KD, Langmead B. Wilks C, et al. Among authors: nellore a. Genome Biol. 2021 Nov 29;22(1):323. doi: 10.1186/s13059-021-02533-6. Genome Biol. 2021. PMID: 34844637 Free PMC article.
Cloud computing for genomic data analysis and collaboration.
Langmead B, Nellore A. Langmead B, et al. Among authors: nellore a. Nat Rev Genet. 2018 Apr;19(4):208-219. doi: 10.1038/nrg.2017.113. Epub 2018 Jan 30. Nat Rev Genet. 2018. PMID: 29379135 Free PMC article. Review.
72 results