[1] |
Anders, S., Pyl, P.T., Huber, W. HTSeq–a Python framework to work with high-throughput sequencing data Bioinformatics, 31 (2015),pp. 166-169
|
[2] |
Bray, N.L., Pimentel, H., Melsted, P. et al. Near-optimal probabilistic RNA-seq quantification Nat. Biotechnol., 34 (2016),pp. 525-527
|
[3] |
Consortium, E.P. An integrated encyclopedia of DNA elements in the human genome Nature, 489 (2012),pp. 57-74
|
[4] |
Di Tommaso, P., Chatzou, M., Floden, E.W. et al. Nextflow enables reproducible computational workflows Nat. Biotechnol., 35 (2017),pp. 316-319
|
[5] |
Ghosh, S., Chan, C.K. Analysis of RNA-seq data using TopHat and Cufflinks Meth. Mol. Biol., 1374 (2016),pp. 339-361
|
[6] |
Gong, Y., Huang, H.T., Liang, Y. et al. lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets BMC Genomics, 18 (2017),p. 434
|
[7] |
Hezroni, H., Koppstein, D., Schwartz, M.G. et al. Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species Cell Rep., 11 (2015),pp. 1110-1122
|
[8] |
Huarte, M. The emerging role of lncRNAs in cancer Nat. Med., 21 (2015),pp. 1253-1261
|
[9] |
Kang, Y.J., Yang, D.C., Kong, L. et al. CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features Nucleic Acids Res., 45 (2017),pp. W12-W16
|
[10] |
Li, A., Zhang, J., Zhou, Z. PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme BMC Bioinf., 15 (2014),p. 311
|
[11] |
Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biol., 15 (2014),p. 550
|
[12] |
McCarthy, D.J., Chen, Y., Smyth, G.K. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation Nucleic Acids Res., 40 (2012),pp. 4288-4297
|
[13] |
Pertea, M., Kim, D., Pertea, G.M. et al. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown Nat. Protoc., 11 (2016),pp. 1650-1667
|
[14] |
Sun, Z., Nair, A., Chen, X. et al. UClncR: ultrafast and comprehensive long non-coding RNA detection from RNA-seq Sci. Rep., 7 (2017)
|
[15] |
Tarazona, S., Furio-Tari, P., Turra, D. et al. Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package Nucleic Acids Res., 43 (2015),p. e140
|
[16] |
Tsoi, L.C., Iyer, M.K., Stuart, P.E. et al. Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin Genome Biol., 16 (2015),p. 24
|
[17] |
Wang, L., Park, H.J., Dasari, S. et al. CPAT: coding-Potential Assessment Tool using an alignment-free logistic regression model Nucleic Acids Res., 41 (2013),p. e74
|
[18] |
Wapinski, O., Chang, H.Y. Long noncoding RNAs and human disease Trends Cell Biol., 21 (2011),pp. 354-361
|
[19] |
Wu, G.C., Pan, H.F., Leng, R.X. et al. Emerging role of long noncoding RNAs in autoimmune diseases Autoimmun. Rev., 14 (2015),pp. 798-805
|
[20] |
Zhang, Q., Chen, L., Cui, S. et al. Expression and regulation of long noncoding RNAs during the osteogenic differentiation of periodontal ligament stem cells in the inflammatory microenvironment Sci. Rep., 7 (2017)
|