1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
|
Source: tnseq-transit
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>,
Étienne Mollier <emollier@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
python3-dev,
python3-setuptools,
python3-numpy,
python3-scipy,
python3-pil,
python3-matplotlib,
python3-sklearn <!nocheck>,
python3-statsmodels,
python3-pubsub,
bwa
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/tnseq-transit
Vcs-Git: https://salsa.debian.org/med-team/tnseq-transit.git
Homepage: http://saclab.tamu.edu/essentiality/transit/
Rules-Requires-Root: no
Package: tnseq-transit
Architecture: any
Depends: ${python3:Depends},
${misc:Depends},
python3-numpy,
python3-scipy,
python3-pil,
python3-matplotlib,
python3-statsmodels,
python3-pubsub,
python3-wxgtk4.0,
bwa
Breaks: transit
Provides: transit
Replaces: transit
Description: statistical calculations of essentiality of genes or genomic regions
This is a software that can be used to analyze Tn-Seq datasets. It
includes various statistical calculations of essentiality of genes or
genomic regions (including conditional essentiality between 2
conditions). These methods were developed and tested as a collaboration
between the Sassetti lab (UMass) and the Ioerger lab (Texas A&M)
.
TRANSIT is capable of analyzing TnSeq libraries constructed with Himar1
or Tn5 datasets.
.
TRANSIT assumes you have already done pre-processing of raw sequencing
files (.fastq) and extracted read counts into a .wig formatted file.
The .wig file should contain the counts at all sites where an insertion
could take place (including sites with no reads). For Himar1 datasets
this is all TA sites in the genome. For Tn5 datasets this would be all
nucleotides in the genome.
|
