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Paket: trinityrnaseq (2.13.2+dfsg-3)

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.

trinityrnaseq ile İlgili Diğer Paketler

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  • 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 (>= 2.34)
    GNU C Library: Shared libraries
    ayrıca şunun tarafından sağlanan bir sanal paket libc6-udeb
  • dep: libgcc-s1 (>= 3.0) [arm64]
    GCC support library
    dep: libgcc-s1 (>= 3.3.1) [amd64]
  • dep: libgetopt-java
    GNU getopt - Java port
  • dep: libgomp1 (>= 6)
    GCC OpenMP (GOMP) support library
  • dep: libhts3 (>= 1.10)
    C library for high-throughput sequencing data formats
  • dep: libjung-free-java
    Java Universal Network/Graph Framework
  • dep: libstdc++6 (>= 11)
    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-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)
    compression library - runtime
  • 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

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Mimari Paket Boyutu Kurulu Boyut Dosyalar
amd64 1.682,3 kB6888 kB [dosya listesi]
arm64 1.651,1 kB7032 kB [dosya listesi]