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[ Source: trinityrnaseq  ]

Links for trinityrnaseq

Ubuntu Resources:

• Bug Reports
• Ubuntu Changelog
• Copyright File

Download Source Package trinityrnaseq:

• [trinityrnaseq_2.15.2+dfsg-1.dsc]
• [trinityrnaseq_2.15.2+dfsg.orig.tar.xz]
• [trinityrnaseq_2.15.2+dfsg-1.debian.tar.xz]

Maintainer:

• Ubuntu MOTU Developers (Mail Archive)

Please consider filing a bug or asking a question via Launchpad before contacting the maintainer directly.

Original Maintainers (usually from Debian):

• Debian Med Packaging Team (Mail Archive)
• Michael R. Crusoe

It should generally not be necessary for users to contact the original maintainer.

External Resources:

• Homepage [github.com]

Similar packages:

• bandage
• bandage-examples
• cufflinks
• crac
• kallisto
• rsem
• berkeley-express-doc
• kallisto-examples
• r-bioc-scuttle
• r-bioc-cummerbund
• r-bioc-deseq2

Other Packages Related to trinityrnaseq

depends

recommends

suggests

enhances

• dep: berkeley-express

  Streaming quantification for high-throughput sequencing

• dep: bowtie

  Ultrafast memory-efficient short read aligner

• dep: bowtie2

  ultrafast memory-efficient short read aligner

• dep: default-jre-headless

  Standard Java or Java compatible Runtime (headless)

• dep: jaligner

  Smith-Waterman algorithm with Gotoh's improvement

• dep: jellyfish

  count k-mers in DNA sequences

• dep: kallisto

  near-optimal RNA-Seq quantification

• dep: libc6 (>= 2.38)

  GNU C Library: Shared libraries

• dep: libgcc-s1 (>= 3.0) [arm64, ppc64el]

  GCC support library

  dep: libgcc-s1 (>= 3.3.1) [amd64]

  dep: libgcc-s1 (>= 3.4) [riscv64]

• dep: libgetopt-java

  GNU getopt - Java port

• dep: libgomp1 (>= 6)

  GCC OpenMP (GOMP) support library

• dep: libhts3t64 (>= 1.17)

  C library for high-throughput sequencing data formats

• dep: libjung-free-java

  Java Universal Network/Graph Framework

• dep: libstdc++6 (>= 14)

  GNU Standard C++ Library v3

• dep: liburi-perl

  module to manipulate and access URI strings

• dep: libwww-perl

  simple and consistent interface to the world-wide web

• dep: ncbi-blast+

  next generation suite of BLAST sequence search tools

• dep: parafly

  parallel command processing using OpenMP

• dep: perl

  Larry Wall's Practical Extraction and Report Language

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: python3-htseq

  Python3 high-throughput genome sequencing read analysis utilities

• dep: r-base-core

  GNU R core of statistical computation and graphics system

• dep: rsem

  RNA-Seq by Expectation-Maximization

• dep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• dep: subread

  toolkit for processing next-gen sequencing data

• dep: trimmomatic

  flexible read trimming tool for Illumina NGS data

• dep: zlib1g (>= 1:1.1.4)

  compression library - runtime

• rec: curl

  command line tool for transferring data with URL syntax

• rec: gmap

  spliced and SNP-tolerant alignment for mRNA and short reads

• rec: hisat2

  graph-based alignment of short nucleotide reads to many genomes

• rec: picard-tools

  Command line tools to manipulate SAM and BAM files

• rec: python3-hisat2

  Python scripts accompanying hisat2

• rec: python3-numpy

  Python library for numerical computations (Python 3)

• rec: r-bioc-biobase

  base functions for Bioconductor

• rec: r-bioc-ctc

  Cluster and Tree Conversion

• rec: r-bioc-deseq2

  R package for RNA-Seq Differential Expression Analysis

• rec: r-bioc-dexseq

  GNU R inference of differential exon usage in RNA-Seq

• rec: r-bioc-edger

  Empirical analysis of digital gene expression data in R

• rec: r-bioc-goseq

  GNU R gene ontology analyser for RNA-seq and other length biased data

• rec: r-bioc-qvalue

  GNU R package for Q-value estimation for FDR control

• rec: r-bioc-rots

  GNU R Teproducibility-Optimized Test Statistic

• rec: r-cran-ape

  GNU R package for Analyses of Phylogenetics and Evolution

• rec: r-cran-argparse

  GNU R command line parser for optional and positional arguments

• rec: r-cran-cluster

  GNU R package for cluster analysis by Rousseeuw et al

• rec: r-cran-fastcluster

  Fast hierarchical clustering routines for GNU R

• rec: r-cran-goplot

  GNU R visualization of functional analysis data

• rec: r-cran-gplots

  GNU R package with tools for plotting data by Greg Warnes et al

• rec: r-cran-kernsmooth

  GNU R package for kernel smoothing and density estimation

• rec: r-cran-readr

  GNU R package to read rectangular text data

• rec: r-cran-tidyverse

  Easily Install and Load the 'Tidyverse'

• rec: rna-star

  ultrafast universal RNA-seq aligner

• rec: salmon

  wicked-fast transcript quantification from RNA-seq data

• rec: tabix

  generic indexer for TAB-delimited genome position files

• rec: trinityrnaseq-examples

  RNA-Seq De novo Assembly common example and testing files

• sug: collectl

  Utility to collect Linux performance data

• sug: r-bioc-tximport

  transcript-level estimates for biological sequencing

• sug: r-bioc-tximportdata

  GNU R various transcript abundance quantifiers

• sug: transdecoder

  find coding regions within RNA transcript sequences

Download trinityrnaseq

Download for all available architectures

Architecture	Package Size	Installed Size	Files
amd64	1,737.1 kB	7,071.0 kB	[list of files]
arm64	1,692.0 kB	7,731.0 kB	[list of files]
ppc64el	1,813.4 kB	8,692.0 kB	[list of files]
riscv64	1,730.6 kB	6,979.0 kB	[list of files]