<s>
dupRadar	O
An	O
R	B-Language
package	I-Language
which	O
provides	O
functions	O
for	O
plotting	O
and	O
analyzing	O
the	O
duplication	O
rates	O
dependent	O
on	O
the	O
expression	O
levels	O
.	O
</s>
<s>
FastQC	O
is	O
a	O
quality	O
control	O
tool	O
for	O
high-throughput	O
sequence	O
data	O
(	O
Babraham	O
Institute	O
)	O
and	O
is	O
developed	O
in	O
Java	B-Device
.	O
</s>
<s>
Results	O
are	O
presented	O
in	O
HTML	B-Language
permanent	O
reports	O
.	O
</s>
<s>
fastqp	O
Simple	O
FASTQ	O
quality	O
assessment	O
using	O
Python	B-Language
.	O
</s>
<s>
HTSeq	O
The	O
Python	B-Language
script	I-Language
htseq-qa	O
takes	O
a	O
file	O
with	O
sequencing	O
reads	O
(	O
either	O
raw	O
or	O
aligned	O
reads	O
)	O
and	O
produces	O
a	O
PDF	O
file	O
with	O
useful	O
plots	O
to	O
assess	O
the	O
technical	O
quality	O
of	O
a	O
run	O
.	O
</s>
<s>
MultiQC	O
-	O
Aggregate	O
and	O
visualise	O
results	O
from	O
numerous	O
tools	O
(	O
FastQC	O
,	O
HTSeq	O
,	O
RSeQC	O
,	O
Tophat	B-Application
,	O
STAR	O
,	O
others	O
..	O
)	O
across	O
all	O
samples	O
into	O
a	O
single	O
report	O
.	O
</s>
<s>
Produces	O
graphical	O
output	O
of	O
statistics	O
for	O
use	O
in	O
quality	O
control	O
pipelines	O
,	O
and	O
an	O
optional	O
HTML	B-Language
quality	O
report	O
.	O
</s>
<s>
RNA-SeQC	O
is	O
implemented	O
in	O
Java	B-Device
and	O
is	O
not	O
required	O
installation	O
,	O
however	O
can	O
be	O
run	O
using	O
the	O
GenePattern	O
web	O
interface	O
.	O
</s>
<s>
HTML	B-Language
reports	O
are	O
generated	O
as	O
output	O
.	O
</s>
<s>
The	O
input	O
can	O
be	O
SAM	O
,	O
BAM	O
,	O
FASTA	B-Application
,	O
BED	O
files	O
or	O
Chromosome	O
size	O
file	O
(	O
two-column	O
,	O
plain	O
text	O
file	O
)	O
.	O
</s>
<s>
However	O
,	O
R	B-Language
scripts	O
can	O
also	O
be	O
used	O
for	O
visualization	O
.	O
</s>
<s>
Interconverts	O
between	O
fastq	O
,	O
fasta	B-Application
,	O
sam	O
,	O
scarf	O
,	O
interleaved	O
and	O
2-file	O
paired	O
,	O
gzipped	O
,	O
bzipped	O
,	O
ASCII-33	O
and	O
ASCII-64	O
.	O
</s>
<s>
Open-source	O
,	O
written	O
in	O
pure	O
Java	B-Device
;	O
supports	O
all	O
platforms	O
with	O
no	O
recompilation	O
and	O
no	O
other	O
dependencies	O
.	O
</s>
<s>
FASTX	O
Toolkit	O
is	O
a	O
set	O
of	O
command	O
line	O
tools	O
to	O
manipulate	O
reads	O
in	O
files	O
FASTA	B-Application
or	O
FASTQ	O
format	O
.	O
</s>
<s>
These	O
commands	O
make	O
possible	O
preprocess	O
the	O
files	O
before	O
mapping	O
with	O
tools	O
like	O
Bowtie	B-Application
.	O
</s>
<s>
Some	O
of	O
the	O
tasks	O
allowed	O
are	O
:	O
conversion	O
from	O
FASTQ	O
to	O
FASTA	B-Application
format	O
,	O
information	O
about	O
statistics	O
of	O
quality	O
,	O
removing	O
sequencing	O
adapters	O
,	O
filtering	O
and	O
cutting	O
sequences	O
based	O
on	O
quality	O
or	O
conversion	O
DNA/RNA	O
.	O
</s>
<s>
htSeqTools	O
is	O
a	O
Bioconductor	B-Application
package	O
able	O
to	O
perform	O
quality	O
control	O
,	O
processing	O
of	O
data	O
and	O
visualization	O
.	O
</s>
<s>
It	O
takes	O
in	O
and	O
returns	O
fastq	O
or	O
fasta	B-Application
formatted	O
sequence	O
files	O
.	O
</s>
<s>
ShortRead	O
is	O
a	O
package	O
provided	O
in	O
the	O
R	B-Language
(	O
programming	O
language	O
)	O
/	O
BioConductor	B-Application
environments	O
and	O
allows	O
input	O
,	O
manipulation	O
,	O
quality	O
assessment	O
and	O
output	O
of	O
next-generation	O
sequencing	O
data	O
.	O
</s>
<s>
ShortRead	O
could	O
be	O
complemented	O
with	O
several	O
Bioconductor	B-Application
packages	O
to	O
further	O
analysis	O
and	O
visualization	O
solutions	O
(	O
BioStrings	O
,	O
BSgenome	O
,	O
IRanges	O
,	O
and	O
so	O
on	O
)	O
.	O
</s>
<s>
fastp	B-Application
A	O
tool	O
designed	O
to	O
provide	O
all-in-one	O
preprocessing	O
for	O
FastQ	O
files	O
.	O
</s>
<s>
FASTX-Toolkit	O
The	O
FASTX-Toolkit	O
is	O
a	O
collection	O
of	O
command	O
line	O
tools	O
for	O
Short-Reads	O
FASTA/FASTQ	O
files	O
preprocessing	O
.	O
</s>
<s>
EDASeq	O
is	O
a	O
Bioconductor	B-Application
package	O
to	O
perform	O
GC-Content	O
Normalization	O
for	O
RNA-Seq	O
Data	O
.	O
</s>
<s>
RUV	O
is	O
a	O
R	B-Language
package	I-Language
that	O
implements	O
the	O
remove	O
unwanted	O
variation	O
(	O
RUV	O
)	O
methods	O
of	O
Risso	O
et	O
al	O
.	O
</s>
<s>
Open-source	O
,	O
written	O
in	O
pure	O
Java	B-Device
;	O
supports	O
all	O
platforms	O
with	O
no	O
recompilation	O
and	O
no	O
other	O
dependencies	O
.	O
</s>
<s>
DeconRNASeq	O
is	O
an	O
R	B-Language
package	I-Language
for	O
deconvolution	O
of	O
heterogeneous	O
tissues	O
based	O
on	O
mRNA-Seq	O
data	O
.	O
</s>
<s>
See	O
also	O
List	B-Application
of	I-Application
sequence	I-Application
alignment	I-Application
software	I-Application
.	O
</s>
<s>
Basically	O
,	O
there	O
are	O
two	O
types	O
:	O
1	O
)	O
based	O
on	O
the	O
Burrows	B-Algorithm
–	I-Algorithm
Wheeler	I-Algorithm
transform	I-Algorithm
method	O
such	O
as	O
Bowtie	B-Application
and	O
BWA	O
,	O
and	O
2	O
)	O
based	O
on	O
Seed-extend	O
methods	O
,	O
Needleman	B-Algorithm
–	I-Algorithm
Wunsch	I-Algorithm
or	O
Smith	B-Algorithm
–	I-Algorithm
Waterman	I-Algorithm
algorithms	I-Algorithm
.	O
</s>
<s>
The	O
first	O
group	O
(	O
Bowtie	B-Application
and	O
BWA	O
)	O
is	O
many	O
times	O
faster	O
,	O
however	O
some	O
tools	O
of	O
the	O
second	O
group	O
tend	O
to	O
be	O
more	O
sensitive	O
,	O
generating	O
more	O
correctly	O
aligned	O
reads	O
.	O
</s>
<s>
BFAST	O
works	O
with	O
the	O
Smith	B-Algorithm
–	I-Algorithm
Waterman	I-Algorithm
algorithm	I-Algorithm
.	O
</s>
<s>
Bowtie	B-Application
is	O
a	O
short	O
aligner	O
using	O
an	O
algorithm	O
based	O
on	O
the	O
Burrows	B-Algorithm
–	I-Algorithm
Wheeler	I-Algorithm
transform	I-Algorithm
and	O
the	O
FM-index	B-Algorithm
.	O
</s>
<s>
Bowtie	B-Application
tolerates	O
a	O
small	O
number	O
of	O
mismatches	O
.	O
</s>
<s>
Bowtie2	O
Bowtie	B-Application
2	O
is	O
a	O
memory-efficient	O
tool	O
for	O
aligning	O
sequencing	O
reads	O
to	O
long	O
reference	O
sequences	O
.	O
</s>
<s>
Bowtie2	O
indexes	O
the	O
genome	O
with	O
an	O
FM-index	B-Algorithm
to	O
keep	O
its	O
memory	O
footprint	O
small	O
:	O
for	O
the	O
human	O
genome	O
,	O
its	O
memory	O
footprint	O
is	O
typically	O
around	O
3.2GB	O
.	O
</s>
<s>
GNUMAP	O
performs	O
alignment	O
using	O
a	O
probabilistic	O
Needleman	B-Algorithm
–	I-Algorithm
Wunsch	I-Algorithm
algorithm	I-Algorithm
.	O
</s>
<s>
Mosaik	O
Mosaik	O
is	O
able	O
to	O
align	O
reads	O
containing	O
short	O
gaps	O
using	O
Smith	B-Algorithm
–	I-Algorithm
Waterman	I-Algorithm
algorithm	I-Algorithm
,	O
ideal	O
to	O
overcome	O
SNPs	O
,	O
insertions	O
and	O
deletions	O
.	O
</s>
<s>
NovoAlign	O
(	O
commercial	O
)	O
is	O
a	O
short	O
aligner	O
to	O
the	O
Illumina	O
platform	O
based	O
on	O
Needleman	B-Algorithm
–	I-Algorithm
Wunsch	I-Algorithm
algorithm	I-Algorithm
.	O
</s>
<s>
SEAL	O
uses	O
a	O
MapReduce	B-Operating_System
model	O
to	O
produce	O
distributed	O
computing	O
on	O
clusters	O
of	O
computers	O
.	O
</s>
<s>
Firstly	O
,	O
the	O
q-gram	B-Language
filtering	O
technique	O
based	O
on	O
multiple	O
seeds	O
identifies	O
candidate	O
regions	O
.	O
</s>
<s>
Secondly	O
,	O
these	O
regions	O
are	O
investigated	O
in	O
detail	O
using	O
Smith	B-Algorithm
–	I-Algorithm
Waterman	I-Algorithm
algorithm	I-Algorithm
.	O
</s>
<s>
RUM	O
performs	O
alignment	O
based	O
on	O
a	O
pipeline	O
,	O
being	O
able	O
to	O
manipulate	O
reads	O
with	O
splice	O
junctions	O
,	O
using	O
Bowtie	B-Application
and	O
Blat	O
.	O
</s>
<s>
The	O
flowchart	O
starts	O
doing	O
alignment	O
against	O
a	O
genome	O
and	O
a	O
transcriptome	O
database	O
executed	O
by	O
Bowtie	B-Application
.	O
</s>
<s>
The	O
input	O
files	O
can	O
be	O
in	O
FASTA	B-Application
or	O
FASTQ	O
format	O
.	O
</s>
<s>
Open-source	O
,	O
written	O
in	O
pure	O
Java	B-Device
;	O
supports	O
all	O
platforms	O
with	O
no	O
recompilation	O
and	O
no	O
other	O
dependencies	O
.	O
</s>
<s>
:	O
TopHat	B-Application
or	O
MapSplice	O
)	O
.	O
</s>
<s>
GMAP	O
A	O
Genomic	O
Mapping	O
and	O
Alignment	B-Application
Program	I-Application
for	O
mRNA	O
and	O
EST	O
Sequences	O
.	O
</s>
<s>
HISAT	O
is	O
a	O
spliced	O
alignment	B-Application
program	I-Application
for	O
mapping	O
RNA-seq	O
reads	O
.	O
</s>
<s>
In	O
addition	O
to	O
one	O
global	O
FM-index	B-Algorithm
that	O
represents	O
a	O
whole	O
genome	O
,	O
HISAT	O
uses	O
a	O
large	O
set	O
of	O
small	O
FM-indexes	B-Algorithm
that	O
collectively	O
cover	O
the	O
whole	O
genome	O
(	O
each	O
index	O
represents	O
a	O
genomic	O
region	O
of	O
~	O
64,000	O
bp	O
and	O
~	O
48,000	O
indexes	O
are	O
needed	O
to	O
cover	O
the	O
human	O
genome	O
)	O
.	O
</s>
<s>
We	O
have	O
developed	O
HISAT	O
based	O
on	O
the	O
Bowtie2	O
implementation	O
to	O
handle	O
most	O
of	O
the	O
operations	O
on	O
the	O
FM-index	B-Algorithm
.	O
</s>
<s>
HISAT2	O
is	O
an	O
alignment	B-Application
program	I-Application
for	O
mapping	O
next-generation	O
sequencing	O
reads	O
(	O
both	O
DNA	O
and	O
RNA	O
)	O
to	O
a	O
population	O
of	O
human	O
genomes	O
(	O
as	O
well	O
as	O
to	O
a	O
single	O
reference	O
genome	O
)	O
.	O
</s>
<s>
2014 ]	O
,	O
we	O
designed	O
and	O
implemented	O
a	O
graph	O
FM-index	B-Algorithm
(	O
GFM	O
)	O
,	O
an	O
original	O
approach	O
and	O
its	O
first	O
implementation	O
to	O
the	O
best	O
of	O
our	O
knowledge	O
.	O
</s>
<s>
This	O
new	O
indexing	O
scheme	O
is	O
called	O
a	O
Hierarchical	O
Graph	O
FM	B-Algorithm
index	I-Algorithm
(	O
HGFM	O
)	O
.	O
</s>
<s>
Firstly	O
,	O
unspliced	O
reads	O
are	O
removed	O
with	O
Bowtie	B-Application
.	O
</s>
<s>
Pass	O
uses	O
Needleman	B-Algorithm
–	I-Algorithm
Wunsch	I-Algorithm
and	O
Smith	B-Algorithm
–	I-Algorithm
Waterman	I-Algorithm
algorithms	I-Algorithm
,	O
and	O
performs	O
alignment	O
in	O
3	O
stages	O
:	O
scanning	O
positions	O
of	O
seed	O
sequences	O
in	O
the	O
genome	O
,	O
testing	O
the	O
contiguous	O
regions	O
and	O
finally	O
refining	O
the	O
alignment	O
.	O
</s>
<s>
TopHat	B-Application
is	O
prepared	O
to	O
find	O
de	O
novo	O
junctions	O
.	O
</s>
<s>
TopHat	B-Application
aligns	O
reads	O
in	O
two	O
steps	O
.	O
</s>
<s>
Firstly	O
,	O
unspliced	O
reads	O
are	O
aligned	O
with	O
Bowtie	B-Application
.	O
</s>
<s>
G.Mo.R-Se	O
is	O
a	O
method	O
that	O
uses	O
RNA-Seq	O
reads	O
to	O
build	O
de	O
novo	O
gene	O
models	O
.	O
</s>
<s>
BaySeq	O
is	O
a	O
Bioconductor	B-Application
package	O
to	O
identify	O
differential	O
expression	O
using	O
next-generation	O
sequencing	O
data	O
,	O
via	O
empirical	O
Bayesian	O
methods	O
.	O
</s>
<s>
casper	O
is	O
a	O
Bioconductor	B-Application
package	O
to	O
quantify	O
expression	O
at	O
the	O
isoform	O
level	O
.	O
</s>
<s>
DESeq	O
is	O
a	O
Bioconductor	B-Application
package	O
to	O
perform	O
differential	O
gene	O
expression	O
analysis	O
based	O
on	O
negative	O
binomial	O
distribution	O
.	O
</s>
<s>
DEXSeq	O
is	O
Bioconductor	B-Application
package	O
that	O
finds	O
differential	O
differential	O
exon	O
usage	O
based	O
on	O
RNA-Seq	O
exon	O
counts	O
between	O
samples	O
.	O
</s>
<s>
DEXUS	O
is	O
a	O
Bioconductor	B-Application
package	O
that	O
identifies	O
differentially	O
expressed	O
genes	O
in	O
RNA-Seq	O
data	O
under	O
all	O
possible	O
study	O
designs	O
such	O
as	O
studies	O
without	O
replicates	O
,	O
without	O
sample	O
groups	O
,	O
and	O
with	O
unknown	O
conditions	O
.	O
</s>
<s>
DGEclust	O
is	O
a	O
Python	B-Language
package	O
for	O
clustering	O
expression	O
data	O
from	O
RNA-seq	O
,	O
CAGE	O
and	O
other	O
NGS	O
assays	O
using	O
a	O
Hierarchical	B-General_Concept
Dirichlet	I-General_Concept
Process	I-General_Concept
Mixture	I-General_Concept
Model	I-General_Concept
.	O
</s>
<s>
EBSeq	O
is	O
a	O
Bioconductor	B-Application
package	O
for	O
identifying	O
genes	O
and	O
isoforms	O
differentially	O
expressed	O
(	O
DE	O
)	O
across	O
two	O
or	O
more	O
biological	O
conditions	O
in	O
an	O
RNA-seq	O
experiment	O
.	O
</s>
<s>
EdgeR	O
is	O
a	O
R	B-Language
package	I-Language
for	O
analysis	O
of	O
differential	O
expression	O
of	O
data	O
from	O
DNA	O
sequencing	O
methods	O
,	O
like	O
RNA-Seq	O
,	O
SAGE	O
or	O
ChIP-Seq	O
data	O
.	O
</s>
<s>
EdgeRun	O
an	O
R	B-Language
package	I-Language
for	O
sensitive	O
,	O
functionally	O
relevant	O
differential	O
expression	O
discovery	O
using	O
an	O
unconditional	O
exact	O
test	O
.	O
</s>
<s>
Although	O
could	O
be	O
coupled	O
directly	O
with	O
aligners	O
(	O
like	O
Bowtie	B-Application
)	O
,	O
eXpress	O
can	O
also	O
be	O
used	O
with	O
de	O
novo	O
assemblers	O
and	O
thus	O
is	O
not	O
needed	O
a	O
reference	O
genome	O
to	O
perform	O
alignment	O
.	O
</s>
<s>
metaseqR	O
is	O
a	O
Bioconductor	B-Application
package	O
that	O
detects	O
differentially	O
expressed	O
genes	O
from	O
RNA-Seq	O
data	O
by	O
combining	O
six	O
statistical	O
algorithms	O
using	O
weights	O
estimated	O
from	O
their	O
performance	O
with	O
simulated	O
data	O
estimated	O
from	O
real	O
data	O
,	O
either	O
public	O
or	O
user-based	O
.	O
</s>
<s>
The	O
pipeline	O
employs	O
tools	O
like	O
Bowtie	B-Application
,	O
TopHat	B-Application
,	O
ArrayExpressHTS	O
and	O
SAMtools	O
.	O
</s>
<s>
Myrna	O
is	O
a	O
pipeline	O
tool	O
that	O
runs	O
in	O
a	O
cloud	O
environment	O
(	O
Elastic	O
MapReduce	B-Operating_System
)	O
or	O
in	O
a	O
unique	O
computer	O
for	O
estimating	O
differential	O
gene	O
expression	O
in	O
RNA-Seq	O
datasets	O
.	O
</s>
<s>
Bowtie	B-Application
is	O
employed	O
for	O
short	O
read	O
alignment	O
and	O
R	B-Language
algorithms	O
for	O
interval	O
calculations	O
,	O
normalization	O
,	O
and	O
statistical	O
processing	O
.	O
</s>
<s>
The	O
exons	O
are	O
aligned	O
and	O
splice	O
junctions	O
are	O
identified	O
using	O
TopHat	B-Application
.	O
</s>
<s>
PANDORA	O
An	O
R	B-Language
package	I-Language
for	O
the	O
analysis	O
and	O
result	O
reporting	O
of	O
RNA-Seq	O
data	O
by	O
combining	O
multiple	O
statistical	O
algorithms	O
.	O
</s>
<s>
QuasR	O
Quantify	O
and	O
Annotate	O
Short	O
Reads	O
in	O
R	B-Language
.	O
</s>
<s>
RNAeXpress	O
Can	O
be	O
run	O
with	O
Java	B-Device
GUI	O
or	O
command	O
line	O
on	O
Mac	O
,	O
Windows	O
,	O
and	O
Linux	O
.	O
</s>
<s>
R	B-Language
package	I-Language
version	O
.	O
</s>
<s>
rQuant	O
is	O
a	O
web	O
service	O
(	O
Galaxy	B-Application
(	O
computational	O
biology	O
)	O
installation	O
)	O
that	O
determines	O
abundances	O
of	O
transcripts	O
per	O
gene	O
locus	O
,	O
based	O
on	O
quadratic	B-Algorithm
programming	I-Algorithm
.	O
</s>
<s>
SAJR	O
is	O
a	O
java-written	O
read	O
counter	O
and	O
R-package	O
for	O
differential	O
splicing	O
analysis	O
.	O
</s>
<s>
Open-source	O
,	O
written	O
in	O
pure	O
Java	B-Device
;	O
supports	O
all	O
platforms	O
with	O
no	O
recompilation	O
and	O
no	O
other	O
dependencies	O
.	O
</s>
<s>
sSeq	O
The	O
purpose	O
of	O
this	O
R	B-Language
package	I-Language
is	O
to	O
discover	O
the	O
genes	O
that	O
are	O
differentially	O
expressed	O
between	O
two	O
conditions	O
in	O
RNA-seq	O
experiments	O
.	O
</s>
<s>
SARTools	O
A	O
DESeq2	O
-	O
and	O
EdgeR-Based	O
R	B-Language
Pipeline	O
for	O
Comprehensive	O
Differential	O
Analysis	O
of	O
RNA-Seq	O
Data	O
.	O
</s>
<s>
Genevestigator	B-Application
by	O
Nebion	O
(	O
basic	O
version	O
is	O
for	O
free	O
for	O
academic	O
researchers	O
)	O
.	O
</s>
<s>
Qlucore	B-Application
.	O
</s>
<s>
ArrayExpressHTS	O
is	O
a	O
BioConductor	B-Application
package	O
that	O
allows	O
preprocessing	O
,	O
quality	O
assessment	O
and	O
estimation	O
of	O
expression	O
of	O
RNA-Seq	O
datasets	O
.	O
</s>
<s>
The	O
package	O
makes	O
use	O
of	O
several	O
tools	O
:	O
ShortRead	O
(	O
quality	O
control	O
)	O
,	O
Bowtie	B-Application
,	O
TopHat	B-Application
or	O
BWA	O
(	O
alignment	O
to	O
a	O
reference	O
genome	O
)	O
,	O
SAMtools	O
format	O
,	O
Cufflinks	O
or	O
MMSEQ	O
(	O
expression	O
estimation	O
)	O
.	O
</s>
<s>
Implemented	O
by	O
Python	B-Language
2.7	O
,	O
BioQueue	O
can	O
work	O
in	O
both	O
POSIX	O
compatible	O
systems	O
(	O
Linux	O
,	O
Solaris	O
,	O
OS	O
X	O
,	O
etc	O
.	O
)	O
</s>
<s>
Currently	O
,	O
DEWE	O
provides	O
two	O
differential	O
expression	O
analysis	O
workflows	O
:	O
HISAT2	O
,	O
StringTie	O
and	O
Ballgown	O
and	O
Bowtie2	O
,	O
StringTie	O
and	O
R	B-Language
libraries	O
(	O
Ballgown	O
and	O
edgeR	O
)	O
.	O
</s>
<s>
Galaxy	B-Application
:	O
Galaxy	B-Application
is	O
a	O
general	O
purpose	O
workbench	O
platform	O
for	O
computational	O
biology	O
.	O
</s>
<s>
GENE-Counter	O
is	O
a	O
Perl	B-Language
pipeline	O
for	O
RNA-Seq	O
differential	O
gene	O
expression	O
analyses	O
.	O
</s>
<s>
Gene-counter	O
performs	O
alignments	O
with	O
CASHX	O
,	O
Bowtie	B-Application
,	O
BWA	O
or	O
other	O
SAM	O
output	O
aligner	O
.	O
</s>
<s>
Results	O
are	O
stored	O
in	O
a	O
MySQL	B-Application
database	O
to	O
make	O
possible	O
additional	O
analyses	O
.	O
</s>
<s>
The	O
MeV	O
modules	O
include	O
a	O
variety	O
of	O
algorithms	O
to	O
execute	O
tasks	O
like	O
Clustering	O
and	O
Classification	O
,	O
Student	B-General_Concept
's	I-General_Concept
t-test	I-General_Concept
,	O
Gene	O
Set	O
Enrichment	O
Analysis	O
or	O
Significance	O
Analysis	O
.	O
</s>
<s>
MeV	O
runs	O
on	O
Java	B-Device
.	O
</s>
<s>
RobiNA	O
provides	O
a	O
user	O
graphical	O
interface	O
to	O
deal	O
with	O
R/BioConductor	O
packages	O
.	O
</s>
<s>
RobiNA	O
provides	O
a	O
package	O
that	O
automatically	O
installs	O
all	O
required	O
external	O
tools	O
(	O
R/Bioconductor	O
frameworks	O
and	O
Bowtie	B-Application
)	O
.	O
</s>
<s>
RobiNA	O
runs	O
on	O
Java	B-Device
version	O
6	O
.	O
</s>
<s>
Taverna	B-Application
is	O
an	O
open	O
source	O
and	O
domain-independent	O
Workflow	O
Management	O
System	O
–	O
a	O
suite	O
of	O
tools	O
used	O
to	O
design	O
and	O
execute	O
scientific	O
workflows	O
and	O
aid	O
in	O
silico	O
experimentation	O
.	O
</s>
<s>
SGSeq	O
A	O
R	B-Language
package	I-Language
to	O
de	O
novo	O
prediction	O
of	O
splicing	O
events	O
.	O
</s>
<s>
SpliceR	O
An	O
R	B-Language
package	I-Language
for	O
classification	O
of	O
alternative	O
splicing	O
and	O
prediction	O
of	O
coding	O
potential	O
from	O
RNA-seq	O
data	O
.	O
</s>
<s>
SpliceSEQ	O
SpliceViewer	O
is	O
a	O
Java	B-Device
application	O
that	O
allows	O
researchers	O
to	O
investigate	O
alternative	O
mRNA	O
splicing	O
patterns	O
in	O
data	O
from	O
high-throughput	O
mRNA	O
sequencing	O
studies	O
.	O
</s>
<s>
IsoformSwitchAnalyzeR	O
IsoformSwitchAnalyzeR	O
is	O
an	O
R	B-Language
package	I-Language
that	O
enables	O
statistical	O
identification	O
of	O
isoform	O
switches	O
with	O
predicted	O
functional	O
consequences	O
where	O
the	O
consequences	O
of	O
interest	O
can	O
be	O
chosen	O
from	O
a	O
long	O
list	O
but	O
includes	O
gain/loss	O
of	O
protein	O
domains	O
,	O
signal	O
peptides	O
changes	O
in	O
NMD	O
sensitivity	O
.	O
</s>
<s>
DRIMSeq	O
An	O
R	B-Language
package	I-Language
that	O
utilizes	O
generalized	O
linear	O
modeling	O
(	O
GLM	O
)	O
to	O
identify	O
isoform	O
switches	O
from	O
estimated	O
isoform	O
count	O
data	O
.	O
</s>
<s>
BayesDRIMSeq	O
An	O
R	B-Language
package	I-Language
containing	O
a	O
Bayesian	O
implementation	O
of	O
DRIMSeq	O
.	O
</s>
<s>
Cufflinks/Cuffdiff	O
Full	O
length	O
isoform/transcript	O
quantification	O
and	O
differential	O
analysis	O
tool	O
which	O
amongst	O
other	O
test	O
for	O
changes	O
in	O
usage	O
for	O
isoform	O
belonging	O
to	O
the	O
same	O
primary	O
transcript	O
(	O
sharing	O
a	O
TSS	O
)	O
via	O
a	O
one-sided	O
t-test	B-General_Concept
based	O
on	O
the	O
asymptotic	O
of	O
the	O
Jensen-Shannon	O
metric	O
.	O
</s>
<s>
rSeqNP	O
An	O
R	B-Language
package	I-Language
that	O
implements	O
a	O
non-parametric	O
approach	O
to	O
test	O
for	O
differential	O
expression	O
and	O
splicing	O
from	O
RNA-Seq	O
data	O
.	O
</s>
<s>
It	O
uses	O
Bowtie	B-Application
as	O
a	O
first	O
aligner	O
and	O
paired-end	O
reads	O
.	O
</s>
<s>
TopHat-Fusion	O
is	O
based	O
on	O
TopHat	B-Application
version	O
and	O
was	O
developed	O
to	O
handle	O
reads	O
resulting	O
from	O
fusion	O
genes	O
.	O
</s>
<s>
It	O
does	O
not	O
require	O
previous	O
data	O
about	O
known	O
genes	O
and	O
uses	O
Bowtie	B-Application
to	O
align	O
continuous	O
reads	O
.	O
</s>
<s>
Sequences	O
alignment	O
are	O
performed	O
by	O
BLAT	O
,	O
calculations	O
are	O
executed	O
by	O
R	B-Language
modules	O
and	O
is	O
fully	O
automated	O
using	O
Perl	B-Language
.	O
</s>
<s>
SCANPY	O
Scalable	O
Python-based	O
implementation	O
for	O
preprocessing	O
,	O
visualization	O
,	O
clustering	O
,	O
trajectory	O
inference	O
and	O
differential	O
expression	O
testing	O
.	O
</s>
<s>
Seurat	O
R	B-Language
package	I-Language
designed	O
for	O
QC	O
,	O
analysis	O
,	O
and	O
exploration	O
of	O
single-cell	O
RNA-seq	O
data	O
.	O
</s>
<s>
Sincell	O
an	O
R/Bioconductor	O
package	O
for	O
statistical	O
assessment	O
of	O
cell-state	O
hierarchies	O
from	O
single-cell	O
RNA-seq	O
.	O
</s>
<s>
BPSC	O
An	O
R	B-Language
package	I-Language
BPSC	O
for	O
model	O
fitting	O
and	O
differential	O
expression	O
analyses	O
of	O
single-cell	O
RNA-seq	O
.	O
</s>
<s>
Polyester	O
This	O
bioconductor	B-Application
package	O
can	O
be	O
used	O
to	O
simulate	O
RNA-seq	O
reads	O
from	O
differential	O
expression	O
experiments	O
with	O
replicates	O
.	O
</s>
<s>
The	O
reads	O
may	O
be	O
paired	O
or	O
unpaired	O
,	O
with	O
arbitrary	O
length	O
and	O
insert	O
size	O
,	O
output	O
in	O
fasta	B-Application
or	O
fastq	O
,	O
RandomReads	O
has	O
a	O
wide	O
selection	O
of	O
options	O
for	O
mutation	O
rates	O
,	O
with	O
individual	O
settings	O
for	O
substitution	O
,	O
deletion	O
,	O
insertion	O
,	O
and	O
N	O
rates	O
and	O
length	O
distributions	O
,	O
annotating	O
reads	O
with	O
their	O
original	O
,	O
unmutated	O
genomic	O
start	O
and	O
stop	O
location	O
.	O
</s>
<s>
Open-source	O
,	O
written	O
in	O
pure	O
Java	B-Device
;	O
supports	O
all	O
platforms	O
with	O
no	O
recompilation	O
and	O
no	O
other	O
dependencies	O
.	O
</s>
<s>
RNASeqReadSimulator	O
contains	O
a	O
set	O
of	O
simple	O
Python	B-Language
scripts	I-Language
,	O
command	O
line	O
driven	O
.	O
</s>
<s>
WGCNA	O
is	O
an	O
R	B-Language
package	I-Language
for	O
weighted	O
correlation	O
network	O
analysis	O
.	O
</s>
<s>
Pigengene	O
is	O
an	O
R	B-Language
package	I-Language
that	O
infers	O
biological	O
information	O
from	O
gene	O
expression	O
profiles	O
.	O
</s>
<s>
DensityMap	O
is	O
a	O
perl	B-Language
tool	O
for	O
the	O
visualization	O
of	O
features	O
density	O
along	O
chromosomes	O
.	O
</s>
<s>
petal	O
Co-expression	O
network	O
modelling	O
in	O
R	B-Language
.	O
</s>
<s>
ToPASeq	O
:	O
an	O
R	B-Language
package	I-Language
for	O
topology-based	O
pathway	O
analysis	O
of	O
microarray	O
and	O
RNA-Seq	O
data	O
.	O
</s>
<s>
This	O
tool	O
is	O
developed	O
in	O
perl	B-Language
and	O
it	O
is	O
available	O
as	O
console	O
tool	O
.	O
</s>
<s>
It	O
comprises	O
mapping	O
RNA-Seq	O
reads	O
against	O
a	O
reference	O
database	O
of	O
HLA	O
alleles	O
using	O
bowtie	B-Application
,	O
determining	O
and	O
reporting	O
HLA	O
type	O
,	O
confidence	O
score	O
and	O
locus-specific	O
expression	O
level	O
.	O
</s>
<s>
This	O
tool	O
is	O
developed	O
in	O
Python	B-Language
and	O
R	B-Language
.	O
It	O
is	O
available	O
as	O
console	O
tool	O
or	O
Galaxy	B-Application
module	O
.	O
</s>
