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
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
|
Source: trinityrnaseq
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <crusoe@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
libjung-free-java (>= 2.1.1),
javahelper,
libgetopt-java,
default-jdk,
libjs-jquery,
jaligner,
libhts-dev,
zlib1g-dev,
cmake
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/trinityrnaseq
Vcs-Git: https://salsa.debian.org/med-team/trinityrnaseq.git
Homepage: https://github.com/trinityrnaseq/trinityrnaseq
Rules-Requires-Root: no
Package: trinityrnaseq
Architecture: amd64 arm64 ppc64el riscv64 loong64
Depends: ${shlibs:Depends},
${misc:Depends},
${perl:Depends},
${java:Depends},
bowtie,
bowtie2,
libwww-perl,
default-jre-headless,
samtools,
jellyfish,
r-base-core,
rsem,
berkeley-express,
trimmomatic,
parafly,
ncbi-blast+,
python3,
liburi-perl,
python3-htseq,
subread,
kallisto
Recommends: ${java:Recommends},
curl,
trinityrnaseq-examples,
picard-tools,
tabix,
gmap,
salmon,
rna-star,
hisat2,
r-cran-tidyverse,
r-cran-readr,
r-bioc-edger,
r-bioc-deseq2,
r-bioc-rots,
r-cran-cluster,
r-cran-fastcluster,
r-bioc-ctc,
r-bioc-goseq,
r-cran-goplot,
r-cran-gplots,
r-bioc-dexseq,
r-cran-ape,
r-bioc-biobase,
r-bioc-qvalue,
r-cran-argparse,
r-cran-kernsmooth,
python3-numpy,
python3-hisat2
Suggests: collectl,
transdecoder,
r-bioc-tximport,
r-bioc-tximportdata
Description: RNA-Seq De novo Assembly
Trinity represents a novel method for the efficient and robust de novo
reconstruction of transcriptomes from RNA-seq data. Trinity combines three
independent software modules: Inchworm, Chrysalis, and Butterfly, applied
sequentially to process large volumes of RNA-seq reads. Trinity partitions
the sequence data into many individual de Bruijn graphs, each representing the
transcriptional complexity at a given gene or locus, and then processes
each graph independently to extract full-length splicing isoforms and to tease
apart transcripts derived from paralogous genes.
Package: trinityrnaseq-examples
Architecture: amd64 arm64 ppc64el riscv64 loong64
Depends: ${perl:Depends},
${java:Depends},
${misc:Depends},
r-base-core
Recommends: trinityrnaseq
Description: RNA-Seq De novo Assembly common example and testing files
Trinity represents a novel method for the efficient and robust de novo
reconstruction of transcriptomes from RNA-seq data. Trinity combines three
independent software modules: Inchworm, Chrysalis, and Butterfly, applied
sequentially to process large volumes of RNA-seq reads. Trinity partitions
the sequence data into many individual de Bruijn graphs, each representing the
transcriptional complexity at a given gene or locus, and then processes
each graph independently to extract full-length splicing isoforms and to tease
apart transcripts derived from paralogous genes.
.
This package contains testing & example files.
|
