Paketti: trinityrnaseq (2.6.6+dfsg-6)

[ Source: trinityrnaseq  ]

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.

Muut pakettiin trinityrnaseq liittyvät paketit

• 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: curl

  command line tool for transferring data with URL syntax

• 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: libc6 (>= 2.27)

  GNU-C-kirjasto: jaetut kirjastot
  myös näennäispaketti, jonka toteuttaa libc6-udeb

• dep: libcommons-collections4-java

  Apache Commons Collections - Extended Collections API for Java

• dep: libgcc1 (>= 1:3.0)

  GCC:n apukirjasto

• dep: libgetopt-java

  GNU getopt - Java port

• dep: libgomp1 (>= 4.9)

  GCC OpenMP (GOMP) support library

• dep: libhts2 (>= 1.0)

  C library for high-throughput sequencing data formats

• dep: libjung-free-java

  Java Universal Network/Graph Framework

• dep: libstdc++6 (>= 5.2)

  GNU standardi C++ -kirjasto, versio 3

• 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 Wallin kieli tekstitiedostojen analysointia ja raportointia varten

• dep: python3-numpy

  Fast array facility to the Python 3 language

• dep: r-base-core

  GNU R core of statistical computation and graphics system

• dep: r-bioc-qvalue

  GNU R package for Q-value estimation for FDR control

• dep: r-cran-cluster

  GNU R package for cluster analysis by Rousseeuw et al

• dep: rsem

  RNA-Seq by Expectation-Maximization

• dep: salmon

  wicked-fast transcript quantification from RNA-seq data

• dep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• dep: transdecoder

  find coding regions within RNA transcript sequences

• dep: trimmomatic

  flexible read trimming tool for Illumina NGS data

• dep: zlib1g (>= 1:1.1.4)

  pakkauskirjaston ajonaikaistiedostot

• rec: trinityrnaseq-examples

  RNA-Seq De novo Assembly common example and testing files

• sug: collectl

  Utility to collect Linux performance data

Imuroi trinityrnaseq

Imurointi kaikille saataville arkkitehtuureille

Arkkitehtuuri	Paketin koko	Koko asennettuna	Tiedostot
amd64	1,794.9 kt	8,883.0 kt	[tiedostoluettelo]