软件包：trinityrnaseq（2.11.0+dfsg-6）

[ 源代码： 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.

其他与 trinityrnaseq 有关的软件包

• 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: gmap

  spliced and SNP-tolerant alignment for mRNA and short reads

• dep: hisat2

  graph-based alignment of short nucleotide reads to many genomes

• 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 (>= 2.27)

  GNU C 语言运行库：共享库
  同时作为一个虚包由这些包填实： libc6-udeb

• dep: libcommons-collections4-java

  Apache Commons Collections - Extended Collections API for Java

• dep: libgcc-s1 (>= 3.0)

  GCC 支持库

• dep: libgetopt-java

  GNU getopt - Java port

• dep: libgomp1 (>= 6)

  GCC OpenMP（GOMP）支持库

• dep: libhts3 (>= 1.10)

  C library for high-throughput sequencing data formats

• dep: libjung-free-java

  Java Universal Network/Graph Framework

• dep: libstdc++6 (>= 9)

  GNU 标准 C++ 库，第3版

• 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

  拉里 沃尔的实用报表提取语言(Perl)

• dep: python3

  交互式高级面向对象语言（默认 python3 版本）

• dep: python3-hisat2

  Python scripts accompanying hisat2

• dep: python3-htseq

  Python3 high-throughput genome sequencing read analysis utilities

• 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-biobase

  base functions for Bioconductor

• dep: r-bioc-ctc

  Cluster and Tree Conversion

• dep: r-bioc-deseq2

  R package for RNA-Seq Differential Expression Analysis

• dep: r-bioc-dexseq

  GNU R inference of differential exon usage in RNA-Seq

• dep: r-bioc-edger

  Empirical analysis of digital gene expression data in R

• dep: r-bioc-goseq

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

• dep: r-bioc-qvalue

  GNU R package for Q-value estimation for FDR control

• dep: r-bioc-rots

  GNU R Teproducibility-Optimized Test Statistic

• dep: r-bioc-tximport

  transcript-level estimates for biological sequencing

• dep: r-cran-ape

  GNU R package for Analyses of Phylogenetics and Evolution

• dep: r-cran-argparse

  GNU R command line parser for optional and positional arguments

• dep: r-cran-cluster

  GNU R package for cluster analysis by Rousseeuw et al

• dep: r-cran-fastcluster

  Fast hierarchical clustering routines for GNU R

• dep: r-cran-goplot

  GNU R visualization of functional analysis data

• dep: r-cran-gplots

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

• dep: r-cran-readr

  GNU R package to read rectangular text data

• dep: rna-star

  ultrafast universal RNA-seq aligner

• 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: subread

  toolkit for processing next-gen sequencing data

• 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)

  压缩库 - 运行时

• rec: picard-tools

  Command line tools to manipulate SAM and BAM files

• rec: r-cran-tidyverse

  Easily Install and Load the 'Tidyverse'

• 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-tximportdata

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硬件架构	软件包大小	安装后大小	文件
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