- Edgren H, Murumagi A, Kangaspeska S,
Nicorici D, Hongisto V, Kleivi K, Rye IH,
Nyberg S, Wolf M, Borresen-Dale AL, Kallio-
niemi O (2011) Identification of fusion genes
in breast cancer by paired-end RNA-sequen-
cing. Genome Biol 12(1):R6. https://doi.
org/10.1186/gb-2011-12-1-r6 - Treutlein B, Brownfield DG, Wu AR, Neff NF,
Mantalas GL, Espinoza FH, Desai TJ, Krasnow
MA, Quake SR (2014) Reconstructing lineage
hierarchies of the distal lung epithelium using
single-cell RNA-seq. Nature 509
(7500):371–375. https://doi.org/10.1038/
nature13173 - Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ
(2008) Deep surveying of alternative splicing
complexity in the human transcriptome by
high-throughput sequencing. Nat Genet 40
(12):1413–1415. https://doi.org/10.1038/
ng.259 - Yang L, Duff MO, Graveley BR, Carmichael
GG, Chen LL (2011) Genomewide characteri-
zation of non-polyadenylated RNAs. Genome
Biol 12(2):R16. https://doi.org/10.1186/
gb-2011-12-2-r16 - Nagalakshmi U, Wang Z, Waern K, Shou C,
Raha D, Gerstein M, Snyder M (2008) The
transcriptional landscape of the yeast genome
defined by RNA sequencing. Science 320
(5881):1344–1349. https://doi.org/10.
1126/science.1158441 - Cloonan N, Forrest AR, Kolle G, Gardiner BB,
Faulkner GJ, Brown MK, Taylor DF, Steptoe
AL, Wani S, Bethel G, Robertson AJ, Perkins
AC, Bruce SJ, Lee CC, Ranade SS, Peckham
HE, Manning JM, McKernan KJ, Grimmond
SM (2008) Stem cell transcriptome profiling
via massive-scale mRNA sequencing. Nat
Methods 5(7):613–619.https://doi.org/10.
1038/nmeth.1223 - Trapnell C, Pachter L, Salzberg SL (2009)
TopHat: discovering splice junctions with
RNA-Seq. Bioinformatics 25(9):1105–1111.
https://doi.org/10.1093/bioinformatics/
btp120 - Li R, Li Y, Kristiansen K, Wang J (2008)
SOAP: short oligonucleotide alignment pro-
gram. Bioinformatics 24(5):713–714.
https://doi.org/10.1093/bioinformatics/
btn025 - Wu TD, Nacu S (2010) Fast and SNP-tolerant
detection of complex variants and splicing in
short reads. Bioinformatics 26(7):873–881.
https://doi.org/10.1093/bioinformatics/
btq057 - Patro R, Mount SM, Kingsford C (2014) Sail-
fish enables alignment-free isoform quantifica-
tion from RNA-seq reads using lightweight
algorithms. Nat Biotechnol 32(5):462–464.
https://doi.org/10.1038/nbt.2862- Bray NL, Pimentel H, Melsted P, Pachter L
(2016) Near-optimal probabilistic RNA-seq
quantification. Nat Biotechnol 34
(5):525–527. https://doi.org/10.1038/nbt.
3519 - Zyprych-Walczak J, Szabelska A,
Handschuh L, Gorczak K, Klamecka K,
Figlerowicz M, Siatkowski I (2015) The impact
of normalization methods on RNA-Seq data
analysis. Biomed Res Int 2015:621690.
https://doi.org/10.1155/2015/621690 - Ringner M (2008) What is principal compo-
nent analysis? Nat Biotechnol 26(3):303–304 - van der Maaten L (2014) Accelerating t-SNE
using Tree-Based Algorithms. J Mach Learn
Res 15:3221–3245 - Goecks J, Nekrutenko A, Taylor J, Galaxy T
(2010) Galaxy: a comprehensive approach for
supporting accessible, reproducible, and trans-
parent computational research in the life
sciences. Genome Biol 11(8):R86. https://
doi.org/10.1186/gb-2010-11-8-r86 - Nelson JW, Sklenar J, Barnes AP, Minnier J
(2017) The START App: a web-based RNAseq
analysis and visualization resource. Bioinfor-
matics 33(3):447–449. https://doi.org/10.
1093/bioinformatics/btw624 - D’Antonio M, D’Onorio De Meo P,
Pallocca M, Picardi E, D’Erchia AM, Calogero
RA, Castrignano T, Pesole G (2015) RAP:
RNA-Seq Analysis Pipeline, a new cloud-
based NGS web application. BMC Genomics
16:S3.https://doi.org/10.1186/1471-2164-
16-S6-S3 - Velmeshev D, Lally P, Magistri M, Faghihi MA
(2016) CANEapp: a user-friendly application
for automated next generation transcriptomic
data analysis. BMC Genomics 17:49.https://
doi.org/10.1186/s12864-015-2346-y - Anders S, Huber W (2010) Differential expres-
sion analysis for sequence count data. Genome
Biol 11(10):R106.https://doi.org/10.1186/
gb-2010-11-10-r106 - Dennis G Jr, Sherman BT, Hosack DA, Yang J,
Gao W, Lane HC, Lempicki RA (2003)
DAVID: Database for Annotation, Visualiza-
tion, and Integrated Discovery. Genome Biol
4(5):P3 - Huang DW, Sherman BT, Lempicki RA (2009)
Systematic and integrative analysis of large gene
lists using DAVID bioinformatics resources.
Nat Protoc 4(1):44–57.https://doi.org/10.
1038/nprot.2008.211 - Young MD, Wakefield MJ, Smyth GK, Oshlack
A (2010) Gene ontology analysis for RNA-seq:
180 Chao Zhang et al.