reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction

[11] Bernhart SH(2018)Accurate SHAPE-directed RNA structure determination Nat Rev Genet 19 615-79

[12] Zu Siederdissen CH(2010)High-throughput determination of RNA structures Bioinformatics 26 139-55

[13] Tafer H(2011)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data Ann Appl Stat 5 1752-74

[14] Flamm C(2013)Measuring reproducibility of high-throughput experiments Bioinformatics 30 1049-20

[15] Stadler PF(2017)Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data Cell Syst 4 568-89

[16] Kawaguchi R(2014)PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays RNA 20 713-21

[17] Kiryu H(2017)Mod-seq: high-throughput sequencing for chemical probing of RNA structure Nat Methods 14 83-9

[18] Kertesz M(2017)Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments Biochemistry 56 4713-79

[19] Wan Y(2018)Interpreting reverse transcriptase termination and mutation events for greater insight into the chemical probing of RNA Genome Biol 19 28-60

[20] Mazor E(2014)PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures Nature 505 706-96

[11] Bernhart SH(2018)Accurate SHAPE-directed RNA structure determination Nat Rev Genet 19 615-79

[12] Zu Siederdissen CH(2010)High-throughput determination of RNA structures Bioinformatics 26 139-55

[13] Tafer H(2011)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data Ann Appl Stat 5 1752-74

[14] Flamm C(2013)Measuring reproducibility of high-throughput experiments Bioinformatics 30 1049-20

[15] Stadler PF(2017)Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data Cell Syst 4 568-89

[16] Kawaguchi R(2014)PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays RNA 20 713-21

[17] Kiryu H(2017)Mod-seq: high-throughput sequencing for chemical probing of RNA structure Nat Methods 14 83-9

[18] Kertesz M(2017)Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments Biochemistry 56 4713-79

[19] Wan Y(2018)Interpreting reverse transcriptase termination and mutation events for greater insight into the chemical probing of RNA Genome Biol 19 28-60

[20] Mazor E(2014)PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures Nature 505 706-96