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MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing.
Kalari KR, Nair AA, Bhavsar JD, O'Brien DR, Davila JI, Bockol MA, Nie J, Tang X, Baheti S, Doughty JB, Middha S, Sicotte H, Thompson AE, Asmann YW, Kocher JP. Kalari KR, et al. Among authors: kocher jp. BMC Bioinformatics. 2014 Jun 27;15:224. doi: 10.1186/1471-2105-15-224. BMC Bioinformatics. 2014. PMID: 24972667 Free PMC article.
PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data.
Wang C, Evans JM, Bhagwate AV, Prodduturi N, Sarangi V, Middha M, Sicotte H, Vedell PT, Hart SN, Oliver GR, Kocher JP, Maurer MJ, Novak AJ, Slager SL, Cerhan JR, Asmann YW. Wang C, et al. Among authors: kocher jp. Bioinformatics. 2014 Sep 15;30(18):2678-80. doi: 10.1093/bioinformatics/btu363. Epub 2014 May 29. Bioinformatics. 2014. PMID: 24876377 Free PMC article.
HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data.
Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP. Yan H, et al. Among authors: kocher jp. BMC Bioinformatics. 2014 Aug 15;15(1):280. doi: 10.1186/1471-2105-15-280. BMC Bioinformatics. 2014. PMID: 25128017 Free PMC article.
RVboost: RNA-seq variants prioritization using a boosting method.
Wang C, Davila JI, Baheti S, Bhagwate AV, Wang X, Kocher JP, Slager SL, Feldman AL, Novak AJ, Cerhan JR, Thompson EA, Asmann YW. Wang C, et al. Among authors: kocher jp. Bioinformatics. 2014 Dec 1;30(23):3414-6. doi: 10.1093/bioinformatics/btu577. Epub 2014 Aug 27. Bioinformatics. 2014. PMID: 25170027 Free PMC article.
Measure transcript integrity using RNA-seq data.
Wang L, Nie J, Sicotte H, Li Y, Eckel-Passow JE, Dasari S, Vedell PT, Barman P, Wang L, Weinshiboum R, Jen J, Huang H, Kohli M, Kocher JP. Wang L, et al. Among authors: kocher jp. BMC Bioinformatics. 2016 Feb 3;17:58. doi: 10.1186/s12859-016-0922-z. BMC Bioinformatics. 2016. PMID: 26842848 Free PMC article.
164 results