TY - JOUR AU - Frazee, A. C. AU - Langmead, B. AU - Leek, J. T. PY - 2011 DA - 2011// TI - ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets JO - BMC Bioinforma VL - 12 UR - https://doi.org/10.1186/1471-2105-12-449 DO - 10.1186/1471-2105-12-449 ID - Frazee2011 ER - TY - STD TI - Nellore A, Collado-Torres L, Jaffe AE, Alquicira-Hernández J, Pritt J, Morton J, et al. Rail-RNA: scalable analysis of RNA-seq splicing and coverage. Bioinformatics. 2016. ID - ref2 ER - TY - STD TI - Stodden V, Leisch F, Peng RD. Implementing Reproducible Research. Boca Raton: CRC Press; 2014. ID - ref3 ER - TY - JOUR AU - Conesa, A. AU - Madrigal, P. AU - Tarazona, S. AU - Gomez-Cabrero, D. AU - Cervera, A. AU - McPherson, A. PY - 2016 DA - 2016// TI - A survey of best practices for RNA-seq data analysis JO - Genome Biol VL - 17 UR - https://doi.org/10.1186/s13059-016-0881-8 DO - 10.1186/s13059-016-0881-8 ID - Conesa2016 ER - TY - JOUR AU - Bhuvaneshwar, K. AU - Sulakhe, D. AU - Gauba, R. AU - Rodriguez, A. AU - Madduri, R. AU - Dave, U. PY - 2015 DA - 2015// TI - A case study for cloud based high throughput analysis of NGS data using the globus genomics system JO - Comput Struct Biotechnol J VL - 13 UR - https://doi.org/10.1016/j.csbj.2014.11.001 DO - 10.1016/j.csbj.2014.11.001 ID - Bhuvaneshwar2015 ER - TY - JOUR AU - Bray, N. L. AU - Pimentel, H. AU - Melsted, P. AU - Pachter, L. PY - 2016 DA - 2016// TI - Near-optimal probabilistic RNA-seq quantification JO - Nat Biotechnol VL - 34 UR - https://doi.org/10.1038/nbt.3519 DO - 10.1038/nbt.3519 ID - Bray2016 ER - TY - STD TI - Pimentel H, Bray N, Puente S, Melsted P, Pachter L. sleuth: inspect your RNA-Seq [Internet]. Available from: http://pachterlab.github.io/sleuth/. Accessed 31 May 2016. UR - http://pachterlab.github.io/sleuth/ ID - ref7 ER - TY - STD TI - Chang W, Cheng J, Allaire JJ, Xie Y, McPherson J, RStudio, et al. shiny: Web Application Framework for R [Internet]. 2016 Available from: https://cran.r-project.org/web/packages/shiny/index.html. Accessed 31 May 2016. UR - https://cran.r-project.org/web/packages/shiny/index.html ID - ref8 ER - TY - JOUR AU - Köster, J. AU - Rahmann, S. PY - 2012 DA - 2012// TI - Snakemake—a scalable bioinformatics workflow engine JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts480 DO - 10.1093/bioinformatics/bts480 ID - Köster2012 ER - TY - JOUR AU - Trapnell, C. AU - Hendrickson, D. G. AU - Sauvageau, M. AU - Goff, L. AU - Rinn, J. L. AU - Pachter, L. PY - 2013 DA - 2013// TI - Differential analysis of gene regulation at transcript resolution with RNA-seq JO - Nat Biotechnol VL - 31 UR - https://doi.org/10.1038/nbt.2450 DO - 10.1038/nbt.2450 ID - Trapnell2013 ER - TY - JOUR AU - Flicek, P. AU - Amode, M. R. AU - Barrell, D. AU - Beal, K. AU - Billis, K. AU - Brent, S. PY - 2014 DA - 2014// TI - Ensembl 2014 JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1196 DO - 10.1093/nar/gkt1196 ID - Flicek2014 ER - TY - STD TI - Preston-Werner T. Jekyll [Internet]. 2016. Available from: https://jekyllrb.com/. Accessed 31 May 2016. UR - https://jekyllrb.com/ ID - ref12 ER - TY - STD TI - Otto M, Thornton J, Rebert C, Thilo J, XhmikosR, Fenkart H, et al. Bootstrap [Internet]. 2016. Available from: http://getbootstrap.com/. Accessed 31 May 2016. UR - http://getbootstrap.com/ ID - ref13 ER - TY - STD TI - SpryMedia. DataTables [Internet]. 2016. Available from: https://datatables.net/. Accessed 31 May 2016. UR - https://datatables.net/ ID - ref14 ER - TY - JOUR AU - Ng, S. -. Y. AU - Soh, B. S. AU - Rodriguez-Muela, N. AU - Hendrickson, D. G. AU - Price, F. AU - Rinn, J. L. PY - 2015 DA - 2015// TI - Genome-wide RNA-Seq of Human Motor Neurons Implicates Selective ER Stress Activation in Spinal Muscular Atrophy JO - Cell Stem Cell VL - 17 UR - https://doi.org/10.1016/j.stem.2015.08.003 DO - 10.1016/j.stem.2015.08.003 ID - Ng2015 ER -